1
|
van der Sleen L, Stevens JA, Marrink SJ, Poolman B, Tych K. Probing the stability and interdomain interactions in the ABC transporter OpuA using single-molecule optical tweezers. Cell Rep 2024; 43:114110. [PMID: 38607912 DOI: 10.1016/j.celrep.2024.114110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 12/11/2023] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
Transmembrane transporter proteins are essential for maintaining cellular homeostasis and, as such, are key drug targets. Many transmembrane transporter proteins are known to undergo large structural rearrangements during their functional cycles. Despite the wealth of detailed structural and functional data available for these systems, our understanding of their dynamics and, consequently, how they function is generally limited. We introduce an innovative approach that enables us to directly measure the dynamics and stability of interdomain interactions of transmembrane proteins using optical tweezers. Focusing on the osmoregulatory ATP-binding cassette transporter OpuA from Lactococcus lactis, we examine the mechanical properties and potential interactions of its substrate-binding domains. Our measurements are performed in lipid nanodiscs, providing a native-mimicking environment for the transmembrane protein. The technique provides high spatial and temporal resolution and allows us to study the functionally relevant motions and interdomain interactions of individual transmembrane transporter proteins in real time in a lipid bilayer.
Collapse
Affiliation(s)
- Lyan van der Sleen
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands
| | - Jan A Stevens
- Molecular Dynamics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands
| | - Siewert J Marrink
- Molecular Dynamics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands
| | - Bert Poolman
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands.
| | - Kasia Tych
- Chemical Biology Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands.
| |
Collapse
|
2
|
Bershawy R, Hafez HS, El-Sakka SS, Hammad A, Soliman MH. The anticancer and anti-inflammatory activity screening of pyridazinone-based analogs against human epidermoid skin cancer with detailed mechanistic analyses. J Biomol Struct Dyn 2023:1-15. [PMID: 37916672 DOI: 10.1080/07391102.2023.2273985] [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: 06/27/2023] [Accepted: 09/07/2023] [Indexed: 11/03/2023]
Abstract
3(2H)-Pyridazinone derivatives based on 4-biphenyl, naphtha-2-yl, pyridine, or piperidine moiety were synthesized and characterized using I-R and 1HNMR spectra. The activity and cytotoxicity of some synthesized compounds on the skin epidermoid cancer cell proliferation and progression were investigated. The pyridazine isomer with pyridine revealed a significant decrease in the level of nitric oxide p < 0.01 than the activity of caffeine phenecyl ester. The activity of the three active isomers recorded significant activity for their total antioxidant content that triggers their ability for the scavenging the oxygen free radicals significantly p < 0.01. Moreover, revealing the pharmaceutical activity of the isomers as anti-inflammatory agents, IL-6, IL10, and IL12 have been decreased by variable significant values. Additionally, the active isomers revealed variable actions on the skin cancer cell to induce apoptosis using annexin V-FITC/PI. Pyridine was the highest isomer to induce late apoptosis and necrosis for the skin cancer cells against the use of cisplatin. Importantly, Molecular modeling experiments including docking and dynamic simulations were done for the most active 3 analogs to explore the ligand binding and stability leading to exploring the structure-activity relationship with biological target PARP1 which showed a good binding propensity to pyridazine binding site which supports the in vitro data. In conclusion, the pyridazine moieties with piperdine, naphthayl, and pyridine have pharmacological activities against skin cancer epidermoid by triggering action in inhibition of the proliferation and progression with an up-regulated apoptotic mechanism that evades the emergence of cisplatin resistance among different cancer cells.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Rana Bershawy
- Department of Chemistry, Faculty of Science, Suez University, Suez, Egypt
| | - Hani S Hafez
- Department of Zoology, Faculty of Science, Suez University, Suez, Egypt
| | - Sahar S El-Sakka
- Department of Chemistry, Faculty of Science, Suez University, Suez, Egypt
| | - Ali Hammad
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Al-Azhar University, Cairo, Egypt
| | - Mohammed H Soliman
- Department of Chemistry, Faculty of Science, Suez University, Suez, Egypt
| |
Collapse
|
3
|
Gautam P, Sinha SK. Theoretical investigation of functional responses of bio-molecular assembly networks. SOFT MATTER 2023; 19:3803-3817. [PMID: 37191191 DOI: 10.1039/d2sm01530g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Cooperative protein-protein and protein-DNA interactions form programmable complex assemblies, often performing non-linear gene regulatory operations involved in signal transductions and cell fate determination. The apparent structure of those complex assemblies is very similar, but their functional response strongly depends on the topology of the protein-DNA interaction networks. Here, we demonstrate how the coordinated self-assembly creates gene regulatory network motifs that corroborate the existence of a precise functional response at the molecular level using thermodynamic and dynamic analyses. Our theoretical and Monte Carlo simulations show that a complex network of interactions can form a decision-making loop, such as feedback and feed-forward circuits, only by a few molecular mechanisms. We characterize each possible network of interactions by systematic variations of free energy parameters associated with the binding among biomolecules and DNA looping. We also find that the higher-order networks exhibit alternative steady states from the stochastic dynamics of each network. We capture this signature by calculating stochastic potentials and attributing their multi-stability features. We validate our findings against the Gal promoter system in yeast cells. Overall, we show that the network topology is vital in phenotype diversity in regulatory circuits.
Collapse
Affiliation(s)
- Pankaj Gautam
- Theoretical and Computational Biophysical Chemistry Group, Department of Chemistry, Indian Institute of Technology Ropar, Rupnagar, Punjab 140001, India.
| | - Sudipta Kumar Sinha
- Theoretical and Computational Biophysical Chemistry Group, Department of Chemistry, Indian Institute of Technology Ropar, Rupnagar, Punjab 140001, India.
| |
Collapse
|
4
|
Muthu SA, Sharma R, Qureshi A, Parvez S, Ahmad B. Mechanistic insights into monomer level prevention of amyloid aggregation of lysozyme by glycyrrhizic acid. Int J Biol Macromol 2023; 227:884-895. [PMID: 36549619 DOI: 10.1016/j.ijbiomac.2022.12.166] [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: 10/19/2022] [Revised: 12/06/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022]
Abstract
As the primary bioactive compound of glycyrrhiza rhizome, the triterpene glycoside conjugate Glycyrrhizic acid (GA) has demonstrated neuroprotective effects in vivo. This study evaluates the effectiveness of GA as an inhibitor of GuHCl-induced amyloid aggregation of hen egg white lysozyme (HEWL). Fibril formation as measured by Thioflavin-T fluorescence, 900 light scattering, and 8-Anilinonaphthalene-1-sulfonic acid (ANS) fluorescence illustrated ∼90 % prevention of fibrils at [GA]/[HEWL] ≥2:1. Images of Transmission electron microscopy evidence for the absence of any fibril or amorphous aggregation products. The spectral characteristics of soluble HEWL were in close resemblance to unfolded monomer. Computational and fluorescence investigations performed to analyse GA-HEWL interactions demonstrated slightly higher affinity of GA to unfolded HEWL and aggregation-prone regions. The likely mechanism of monomer level aggregation prevention by GA as dermined by computational, stability, and ANS experiments illustrated that GA modulated the compactness, solvent-accessible surface, and solvent-exposed hydrophobic surfaces of aggregation-prone state of HEWL. Our findings corroborate GA as an effective inhibitor of HEWL amyloid formation. To our knowledge, GA interaction-induced inhibition of aggregation-prone states has not been previously discussed. GA's modulation of aggregation-prone states of disease-related proteins will successfully develop GA as an amyloid inhibitor for clinical trials of amyloidosis and neurodegenerative illnesses.
Collapse
Affiliation(s)
- Shivani A Muthu
- Protein Assembly Laboratory, Department of Medical Entomology and Toxicology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India; Department of Molecular Medicine, School of Interdisciplinary Studies, Jamia Hamdard, New Delhi 110062, India
| | - Rahul Sharma
- Department of Molecular Medicine, School of Interdisciplinary Studies, Jamia Hamdard, New Delhi 110062, India
| | - Afnaan Qureshi
- Protein Assembly Laboratory, Department of Medical Entomology and Toxicology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India
| | - Suhel Parvez
- Department of Medical Entomology and Toxicology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India
| | - Basir Ahmad
- Protein Assembly Laboratory, Department of Medical Entomology and Toxicology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India.
| |
Collapse
|
5
|
Musa A, Ihmaid SK, Hughes DL, Said MA, Abulkhair HS, El-Ghorab AH, Abdelgawad MA, Shalaby K, Shaker ME, Alharbi KS, Alotaibi NH, Kays DL, Taylor LJ, Parambi DGT, Alzarea SI, Al-Karmalawy AA, Ahmed HEA, El-Agrody AM. The anticancer and EGFR-TK/CDK-9 dual inhibitory potentials of new synthetic pyranopyrazole and pyrazolone derivatives: X-ray crystallography, in vitro, and in silico mechanistic investigations. J Biomol Struct Dyn 2023; 41:12411-12425. [PMID: 36661285 DOI: 10.1080/07391102.2023.2167000] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 01/03/2023] [Indexed: 01/21/2023]
Abstract
Treatment options for the management of breast cancer are still inadequate. This inadequacy is attributed to the lack of effective targeted medications, often resulting in the recurrence of metastatic disorders. Cumulative evidence suggests that epidermal growth factor receptor (EGFR-TK) and cyclin-dependent kinases-9 (CDK-9) overexpression correlates with worse overall survival in breast cancer patients. Pyranopyrazole and pyrazolone are privileged options for the development of anticancer agents. Inspired by this proven scientific fact, we report here the synthesis of two new series of suggested anticancer molecules incorporating both heterocycles together with their characterization by IR, 1H NMR, 13C NMR, 13C NMR-DEPT, and X-ray diffraction methods. An attempt to get the pyranopyrazole-gold complexes was conducted but unexpectedly yielded benzylidene-2,4-dihydro-3H-pyrazol-3-one instead. This unexpected result was confirmed by X-ray crystallographic analysis. All newly synthesized compounds were assessed for their anti-proliferative activity against two different human breast cancer cells, and the obtained results were compared with the reference drug Staurosporine. The target compounds revealed variable cytotoxicity with IC50 at a low micromolar range with superior selectivity indices. Target enzyme EGFR-TK and CDK-9 assays showed that compounds 22 and 23 effectively inhibited both biological targets with IC50 values of 0.143 and 0.121 µM, respectively. Molecular docking experiments and molecular dynamics simulation were also conducted to further rationalize the in vitro obtained results.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Arafa Musa
- Department of Pharmacognosy, College of Pharmacy, Jouf University, Sakaka, Aljouf, Saudi Arabia
| | - Saleh K Ihmaid
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Jadara University, Irbid, Jordon
| | - David L Hughes
- School of Chemistry, University of East Anglia, Norwich, UK
| | - Musa A Said
- Chemistry Department, College of Sciences, Taibah University, Medina, Saudi Arabia
| | - Hamada S Abulkhair
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Al-Azhar University, Cairo, Egypt
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Horus University-Egypt, International Coastal Road, New Damietta, Egypt
| | - Ahmed H El-Ghorab
- Department of Chemistry, College of Science, Jouf university, Sakaka, Aljouf, Saudi Arabia
| | - Mohamed A Abdelgawad
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf university, Sakaka, Aljouf, Saudi Arabia
| | - Khaled Shalaby
- Department of Pharmaceutics, College of Pharmacy, Jouf University, Sakaka, Saudi Arabia
| | - Mohamed E Shaker
- Department of Pharmacology, College of Pharmacy, Jouf University, Sakaka, Aljouf, Saudi Arabia
| | - Khalid Saad Alharbi
- Department of Pharmacology, College of Pharmacy, Jouf University, Sakaka, Aljouf, Saudi Arabia
| | - Nasser Hadal Alotaibi
- Department of Clinical Pharmacy, College of Pharmacy, Jouf University, Sakaka, Aljouf, Saudi Arabia
| | - Deborah L Kays
- School of Chemistry, University of Nottingham, University Park, Nottingham, UK
| | - Laurence J Taylor
- School of Chemistry, University of Nottingham, University Park, Nottingham, UK
| | - Della Grace Thomas Parambi
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf university, Sakaka, Aljouf, Saudi Arabia
| | - Sami I Alzarea
- Department of Pharmacology, College of Pharmacy, Jouf University, Sakaka, Aljouf, Saudi Arabia
| | - Ahmed A Al-Karmalawy
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ahram Canadian University, Giza, Egypt
| | - Hany E A Ahmed
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Al-Azhar University, Cairo, Egypt
| | - Ahmed M El-Agrody
- Chemistry Department, Faculty of Science, Al-Azhar University, Cairo, Egypt
| |
Collapse
|
6
|
Malebari AM, E A Ahmed H, Ihmaid SK, Omar AM, Muhammad YA, Althagfan SS, Aljuhani N, A A El-Sayed AA, Halawa AH, El-Tahir HM, Turkistani SA, Almaghrabi M, K B Aljohani A, El-Agrody AM, Abulkhair HS. Exploring the dual effect of novel 1,4-diarylpyranopyrazoles as antiviral and anti-inflammatory for the management of SARS-CoV-2 and associated inflammatory symptoms. Bioorg Chem 2023; 130:106255. [PMID: 36403336 PMCID: PMC9671780 DOI: 10.1016/j.bioorg.2022.106255] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 10/30/2022] [Accepted: 11/02/2022] [Indexed: 11/18/2022]
Abstract
COVID-19 and associated substantial inflammations continue to threaten humankind triggering death worldwide. So, the development of new effective antiviral and anti-inflammatory medications is a major scientific goal. Pyranopyrazoles have occupied a crucial position in medicinal chemistry because of their biological importance. Here, we report the design and synthesis of a series of sixteen pyranopyrazole derivatives substituted with two aryl groups at N-1 and C-4. The designed compounds are suggested to show dual activity to combat the emerging Coronaviruses and associated substantial inflammations. All compounds were evaluated for their in vitro antiviral activity and cytotoxicity against SARS-CoV infected Vero cells. As well, the in vitro assay of all derivatives against the SARS-CoV Mpro target was performed. Results revealed the potential of three pyranopyrazoles (22, 27, and 31) to potently inhibit the viral main protease with IC50 values of 2.01, 1.83, and 4.60 μM respectively compared with 12.85 and 82.17 μM for GC-376 and lopinavir. Additionally, in vivo anti-inflammatory testing for the most active compound 27 proved its ability to reduce levels of two cytokines (TNF-α and IL-6). Molecular docking and dynamics simulation revealed consistent results with the in vitro enzymatic assay and indicated the stability of the putative complex of 27 with SARS-CoV-2 Mpro. The assessment of metabolic stability and physicochemical properties of 27 have also been conducted. This investigation identified a set of metabolically stable pyranopyrazoles as effective anti-SARS-CoV-2 Mpro and suppressors of host cell cytokine release. We believe that the new compounds deserve further chemical optimization and evaluation for COVID-19 treatment.
Collapse
Affiliation(s)
- Azizah M Malebari
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Alsulaymanyah, Jeddah 21589, Saudi Arabia
| | - Hany E A Ahmed
- Pharmacognosy and Pharmaceutical Chemistry Department, College of Pharmacy, Taibah University, Al-Madinah Al-Munawarah, Saudi Arabia; Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Al-Azhar University, Nasr City 11884, Cairo, Egypt.
| | - Saleh K Ihmaid
- Pharmacognosy and Pharmaceutical Chemistry Department, College of Pharmacy, Taibah University, Al-Madinah Al-Munawarah, Saudi Arabia; Pharmaceutical Chemistry Department, Faculty of Pharmacy, Jadara University Irbid, Jordan
| | - Abdelsattar M Omar
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Alsulaymanyah, Jeddah 21589, Saudi Arabia; Center for Artificial Intelligence in Precision Medicines, King Abdulaziz University, Jeddah, Saudi Arabia; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Al-Azhar University, Nasr City, Cairo, Egypt
| | - Yosra A Muhammad
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Alsulaymanyah, Jeddah 21589, Saudi Arabia
| | - Sultan S Althagfan
- Clinical and Hospital Pharmacy Department, Taibah University, College of Pharmacy, Taibah University, Al-Madinah Al-Munawarah, Saudi Arabia
| | - Naif Aljuhani
- Pharmacology and Toxicology Department, College of Pharmacy, Taibah University, Al-Madinah Al-Munawarah, Saudi Arabia
| | - Abdel-Aziz A A El-Sayed
- Biology Department, Faculty of Science, Islamic University of Madinah, Madinah, Saudi Arabia; Zoology Department, Faculty of Science, Zagazig University, Zagazig, Egypt
| | - Ahmed H Halawa
- Chemistry Department, Faculty of Science, Al-Azhar University, Nasr City, Cairo, Egypt
| | - Heba M El-Tahir
- Pharmacology and Toxicology Department, College of Pharmacy, Taibah University, Al-Madinah Al-Munawarah, Saudi Arabia
| | | | - Mohammed Almaghrabi
- Pharmacognosy and Pharmaceutical Chemistry Department, College of Pharmacy, Taibah University, Al-Madinah Al-Munawarah, Saudi Arabia
| | - Ahmed K B Aljohani
- Pharmacognosy and Pharmaceutical Chemistry Department, College of Pharmacy, Taibah University, Al-Madinah Al-Munawarah, Saudi Arabia
| | - Ahmed M El-Agrody
- Chemistry Department, Faculty of Science, Al-Azhar University, Nasr City, Cairo, Egypt
| | - Hamada S Abulkhair
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Al-Azhar University, Nasr City 11884, Cairo, Egypt; Pharmaceutical Chemistry Department, Faculty of Pharmacy, Horus University-Egypt, International Coastal Road, New Damietta 34518, Egypt.
| |
Collapse
|
7
|
Mathew B, Oh JM, Abdelgawad MA, Khames A, Ghoneim MM, Kumar S, Nath LR, Sudevan ST, Parambi DGT, Agoni C, Soliman MES, Kim H. Conjugated Dienones from Differently Substituted Cinnamaldehyde as Highly Potent Monoamine Oxidase-B Inhibitors: Synthesis, Biochemistry, and Computational Chemistry. ACS OMEGA 2022; 7:8184-8197. [PMID: 35284720 PMCID: PMC8908507 DOI: 10.1021/acsomega.2c00397] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 02/11/2022] [Indexed: 02/08/2023]
Abstract
Fifteen multiconjugated dienones (MK1-MK15) were synthesized and evaluated to determine their inhibitory activities against monoamine oxidases (MAOs) A and B. All derivatives were found to be potent and highly selective MAO-B inhibitors. Compound MK6, with an IC50 value of 2.82 nM, most effectively inhibited MAO-B, like MK12 (IC50 = 3.22 nM), followed by MK5, MK13, and MK14 (IC50 = 4.02, 4.24, and 4.89 nM, respectively). The selectivity index values of MK6 and MK12 for MAO-B over MAO-A were 7361.5 and 1780.5, respectively. Compounds MK6 and MK12 were competitive reversible inhibitors of MAO-B, with K i values of 1.10 ± 0.20 and 3.0 ± 0.27 nM, respectively. Cytotoxic studies showed that MK5, MK6, MK12, and MK14 exhibited low toxicities on Vero cells, with IC50 values of 218.4, 149.1, 99.96, and 162.3 μg/mL, respectively, which were much higher than those for their effective nanomolar-level concentrations. Also, MK5, MK6, MK12, and MK14 decreased cell damage in H2O2-induced cells via a significant scavenging effect of reactive oxygen species. Molecular modeling was performed to rationalize the potential inhibitory activities of MK5, MK6, MK12, and MK14 toward MAO-B and their possible binding mechanisms, showing high-affinity binding pocket interactions and conformation perturbations of the compounds with MAO-B, which were interpreted as the conformational dynamics of MAO-B. This study concluded that all the compounds tested were more potent MAO-B inhibitors than the reference drugs, and leading compounds could be further explored for their effectiveness in various kinds of neurodegenerative disorders.
Collapse
Affiliation(s)
- Bijo Mathew
- Department
of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi 682041, India
- ,
| | - Jong Min Oh
- Department
of Pharmacy, and Research Institute of Life Pharmaceutical Sciences, Sunchon National University, Suncheon 57922, Republic of Korea
| | - Mohamed A. Abdelgawad
- Department
of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka, Al Jouf 72341, Saudi Arabia
| | - Ahmed Khames
- Department
of Pharmaceutics and Industrial Pharmacy, College of Pharmacy, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Mohammed M. Ghoneim
- Department
of Pharmacy Practice, Faculty of Pharmacy, AlMaarefa University, Ad Diriyah 13713, Saudi Arabia
| | - Sunil Kumar
- Department
of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi 682041, India
| | - Lekshmi R. Nath
- Department
of Pharmacognosy, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi 682041, India
| | - Sachithra Thazhathuveedu Sudevan
- Department
of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi 682041, India
| | - Della Grace Thomas Parambi
- Department
of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka, Al Jouf 72341, Saudi Arabia
| | - Clement Agoni
- Molecular
Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South
Africa
| | - Mahmoud E. S. Soliman
- Molecular
Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South
Africa
| | - Hoon Kim
- Department
of Pharmacy, and Research Institute of Life Pharmaceutical Sciences, Sunchon National University, Suncheon 57922, Republic of Korea
| |
Collapse
|
8
|
Ihmaid SK, Aljuhani A, Alsehli M, Rezki N, Alawi A, Aldhafiri AJ, Salama SA, Ahmed HE, Aouad MR. Discovery of triaromatic flexible agents bearing 1,2,3-Triazole with selective and potent anti-breast cancer activity and CDK9 inhibition supported by molecular dynamics. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131568] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
9
|
Sama-ae I, Sangkanu S, Siyadatpanah A, Norouzi R, Chuprom J, Mitsuwan W, Surinkaew S, Boonhok R, Paul AK, Mahboob T, Abtahi NS, Jimoh TO, Oliveira SM, Gupta M, Sin C, de Lourdes Pereira M, Wilairatana P, Wiart C, Rahmatullah M, Dolma KG, Nissapatorn V. Targeting Acanthamoeba proteins interaction with flavonoids of Propolis extract by in vitro and in silico studies for promising therapeutic effects. F1000Res 2022; 11:1274. [PMID: 36936052 PMCID: PMC10015121 DOI: 10.12688/f1000research.126227.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/25/2022] [Indexed: 11/09/2022] Open
Abstract
Background : Propolis is a natural resinous mixture produced by bees. It provides beneficial effects on human health in the treatment/management of many diseases. The present study was performed to demonstrate the anti- Acanthamoeba activity of ethanolic extracts of Propolis samples from Iran. The interactions of the compounds and essential proteins of Acanthamoeba were also visualized through docking simulation. Methods: The minimal inhibitory concentrations (MICs) of Propolis extract against Acanthamoeba trophozoites and cysts was determined in vitro. In addition, two-fold dilutions of each of the agents were tested for encystment, excystment and adhesion inhibitions. Three major compounds of Propolis extract such as chrysin, tectochrysin and pinocembrin have been selected in molecular docking approach to predict the compounds that might be responsible for encystment, excystment and adhesion inhibitions of A. castellanii. Furthermore, to confirm the docking results, molecular dynamics (MD) simulations were also carried out for the most promising two ligand-pocket complexes from docking studies. Results : The minimal inhibitory concentrations (MICs) 62.5 and 125 µg/mL of the most active Propolis extract were assessed in trophozoites stage of Acanthamoeba castellanii ATCC30010 and ATCC50739, respectively. At concentrations lower than their MICs values (1/16 MIC), Propolis extract revealed inhibition of encystation. However, at 1/2 MIC, it showed a potential inhibition of excystation and anti-adhesion. The molecular docking and dynamic simulation revealed the potential capability of Pinocembrin to form hydrogen bonds with A. castellanii Sir2 family protein (AcSir2), an encystation protein of high relevance for this process in Acanthamoeba. Conclusions : The results obtained provided a candidate for the development of therapeutic drugs against Acanthamoeba infection. In vivo experiments and clinical trials are necessary to support this claim.
Collapse
Affiliation(s)
- Imran Sama-ae
- Department of Medical Technology, School of Allied Health Sciences and Center of Excellence Research for Melioidosis and Microorganisms (CERMM), Walailak University, Nakhon Si Thammarat, Thailand
| | - Suthinee Sangkanu
- School of Allied Health Sciences, Southeast Asia Water Team (SEA Water Team) and World Union for Herbal Drug Discovery (WUHeDD), Walailak University, Nakhon Si Thammarat, Thailand
| | - Abolghasem Siyadatpanah
- Ferdows School of Paramedical and Health, Birjand University of Medical Sciences, Birjand, Iran
- Department of Microbiology, School of Medicine, Infectious Diseases Research Center, Gonabad University of Medical Sciences, Gonabad, Iran
| | - Roghayeh Norouzi
- Department of Pathobiology, Faculty of Veterinary Medicine, University of Tabriz, Tabriz, Iran
| | - Julalak Chuprom
- School of Allied Health Sciences, Southeast Asia Water Team (SEA Water Team) and World Union for Herbal Drug Discovery (WUHeDD), Walailak University, Nakhon Si Thammarat, Thailand
| | - Watcharapong Mitsuwan
- Akkhraratchakumari Veterinary College and Research Center of Excellence in Innovation of Essential Oil, Walailak University, Nakhon Si Thammarat, Thailand
| | - Sirirat Surinkaew
- Department of Medical Technology, School of Allied Health Sciences and Research Excellence Center for Innovation and Health Products (RECIHP), Walailak University, Nakhon Si Thammarat, Thailand
| | - Rachasak Boonhok
- Department of Medical Technology, School of Allied Health Sciences and Research Excellence Center for Innovation and Health Products (RECIHP), Walailak University, Nakhon Si Thammarat, Thailand
| | - Alok K. Paul
- School of Pharmacy and Pharmacology, University of Tasmania, TAS, Australia
| | - Tooba Mahboob
- School of Allied Health Sciences, Southeast Asia Water Team (SEA Water Team) and World Union for Herbal Drug Discovery (WUHeDD), Walailak University, Nakhon Si Thammarat, Thailand
| | - Najme Sadat Abtahi
- Department of Clinical Biochemistry, Faculty of Medicine International Campus, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Tajudeen O. Jimoh
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
- Department of Biochemistry, Faculty of Health Sciences, Islamic University in Uganda, Kampala, Uganda
| | - Sónia M.R. Oliveira
- CICECO-Aveiro Institute of Materials, University of Aveiro, Aveiro, Portugal
- Hunter Medical Research Institute, NSW, Australia
| | - Madhu Gupta
- Department of Pharmaceutics, Delhi Pharmaceutical Sciences and Research University, New Delhi, India
| | - Chea Sin
- Faculty of Pharmacy, University of Puthisastra, Phnom Penh, Cambodia
| | - Maria de Lourdes Pereira
- CICECO-Aveiro Institute of Materials, University of Aveiro, Aveiro, Portugal
- Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Polrat Wilairatana
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Christophe Wiart
- Institute for Tropical Biology & Conservation, University Malaysia Sabah, Sabah, Malaysia
| | - Mohammed Rahmatullah
- Department of Biotechnology & Genetic Engineering, University of Development Alternative, Dhaka, Bangladesh
| | - Karma G. Dolma
- Department of Microbiology, Sikkim Manipal Institute of Medical Sciences, Sikkim Manipal University, Sikkim, India
| | - Veeranoot Nissapatorn
- School of Allied Health Sciences, Southeast Asia Water Team (SEA Water Team) and World Union for Herbal Drug Discovery (WUHeDD), Walailak University, Nakhon Si Thammarat, Thailand
| |
Collapse
|
10
|
Sama-ae I, Sangkanu S, Siyadatpanah A, Norouzi R, Chuprom J, Mitsuwan W, Surinkaew S, Boonhok R, Paul AK, Mahboob T, Abtahi NS, Jimoh TO, Oliveira SM, Gupta M, Sin C, de Lourdes Pereira M, Wilairatana P, Wiart C, Rahmatullah M, Dolma KG, Nissapatorn V. Targeting Acanthamoeba proteins interaction with flavonoids of Propolis extract by in vitro and in silico studies for promising therapeutic effects. F1000Res 2022; 11:1274. [PMID: 36936052 PMCID: PMC10015121.3 DOI: 10.12688/f1000research.126227.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/15/2023] [Indexed: 03/29/2023] Open
Abstract
Background : Propolis is a natural resinous mixture produced by bees. It provides beneficial effects on human health in the treatment/management of many diseases. The present study was performed to demonstrate the anti- Acanthamoeba activity of ethanolic extracts of Propolis samples from Iran. The interactions of the compounds and essential proteins of Acanthamoeba were also visualized through docking simulation. Methods: The minimal inhibitory concentrations (MICs) of Propolis extract against Acanthamoeba trophozoites and cysts was determined in vitro. In addition, two-fold dilutions of each of agents were tested for encystment, excystment and adhesion inhibitions. Three major compounds of Propolis extract such as chrysin, tectochrysin and pinocembrin have been selected in molecular docking approach to predict the compounds that might be responsible for encystment, excystment and adhesion inhibitions of A. castellanii. Furthermore, to confirm the docking results, molecular dynamics (MD) simulations were also carried out for the most promising two ligand-pocket complexes from docking studies. Results : The minimal inhibitory concentrations (MICs) 62.5 and 125 µg/mL of the most active Propolis extract were assessed in trophozoites stage of Acanthamoeba castellanii ATCC30010 and ATCC50739, respectively. At concentrations lower than their MICs values (1/16 MIC), Propolis extract revealed inhibition of encystation. However, at 1/2 MIC, it showed a potential inhibition of excystation and anti-adhesion. The molecular docking and dynamic simulation revealed the potential capability of Pinocembrin to form hydrogen bonds with A. castellanii Sir2 family protein (AcSir2), an encystation protein of high relevance for this process in Acanthamoeba. Conclusions : The results provided a candidate for the development of therapeutic drugs against Acanthamoeba infection. In vivo experiments and clinical trials are necessary to support this claim.
Collapse
Affiliation(s)
- Imran Sama-ae
- Department of Medical Technology, School of Allied Health Sciences and Center of Excellence Research for Melioidosis and Microorganisms (CERMM), Walailak University, Nakhon Si Thammarat, Thailand
| | - Suthinee Sangkanu
- School of Allied Health Sciences, Southeast Asia Water Team (SEA Water Team) and World Union for Herbal Drug Discovery (WUHeDD), Walailak University, Nakhon Si Thammarat, Thailand
| | - Abolghasem Siyadatpanah
- Department of Microbiology, School of Medicine, Infectious Diseases Research Center, Gonabad University of Medical Sciences, Gonabad, Iran
- Ferdows School of Paramedical and Health, Birjand University of Medical Sciences, Birjand, Iran
| | - Roghayeh Norouzi
- Department of Pathobiology, Faculty of Veterinary Medicine, University of Tabriz, Tabriz, Iran
| | - Julalak Chuprom
- School of Allied Health Sciences, Southeast Asia Water Team (SEA Water Team) and World Union for Herbal Drug Discovery (WUHeDD), Walailak University, Nakhon Si Thammarat, Thailand
| | - Watcharapong Mitsuwan
- Akkhraratchakumari Veterinary College and Research Center of Excellence in Innovation of Essential Oil, Walailak University, Nakhon Si Thammarat, Thailand
| | - Sirirat Surinkaew
- Department of Medical Technology, School of Allied Health Sciences and Research Excellence Center for Innovation and Health Products (RECIHP), Walailak University, Nakhon Si Thammarat, Thailand
| | - Rachasak Boonhok
- Department of Medical Technology, School of Allied Health Sciences and Research Excellence Center for Innovation and Health Products (RECIHP), Walailak University, Nakhon Si Thammarat, Thailand
| | - Alok K. Paul
- School of Pharmacy and Pharmacology, University of Tasmania, TAS, Australia
| | - Tooba Mahboob
- School of Allied Health Sciences, Southeast Asia Water Team (SEA Water Team) and World Union for Herbal Drug Discovery (WUHeDD), Walailak University, Nakhon Si Thammarat, Thailand
| | - Najme Sadat Abtahi
- Department of Clinical Biochemistry, Faculty of Medicine International Campus, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Tajudeen O. Jimoh
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
- Department of Biochemistry, Faculty of Health Sciences, Islamic University in Uganda, Kampala, Uganda
| | - Sónia M.R. Oliveira
- CICECO-Aveiro Institute of Materials, University of Aveiro, Aveiro, Portugal
- Hunter Medical Research Institute, NSW, Australia
| | - Madhu Gupta
- Department of Pharmaceutics, Delhi Pharmaceutical Sciences and Research University, New Delhi, India
| | - Chea Sin
- Faculty of Pharmacy, University of Puthisastra, Phnom Penh, Cambodia
| | - Maria de Lourdes Pereira
- CICECO-Aveiro Institute of Materials, University of Aveiro, Aveiro, Portugal
- Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Polrat Wilairatana
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Christophe Wiart
- Institute for Tropical Biology & Conservation, University Malaysia Sabah, Sabah, Malaysia
| | - Mohammed Rahmatullah
- Department of Biotechnology & Genetic Engineering, University of Development Alternative, Dhaka, Bangladesh
| | - Karma G. Dolma
- Department of Microbiology, Sikkim Manipal Institute of Medical Sciences, Sikkim Manipal University, Sikkim, India
| | - Veeranoot Nissapatorn
- School of Allied Health Sciences, Southeast Asia Water Team (SEA Water Team) and World Union for Herbal Drug Discovery (WUHeDD), Walailak University, Nakhon Si Thammarat, Thailand
| |
Collapse
|
11
|
Sama-ae I, Sangkanu S, Siyadatpanah A, Norouzi R, Chuprom J, Mitsuwan W, Surinkaew S, Boonhok R, Paul AK, Mahboob T, Abtahi NS, Jimoh TO, Oliveira SM, Gupta M, Sin C, de Lourdes Pereira M, Wilairatana P, Wiart C, Rahmatullah M, Dolma KG, Nissapatorn V. Targeting Acanthamoeba proteins interaction with flavonoids of Propolis extract by in vitro and in silico studies for promising therapeutic effects. F1000Res 2022; 11:1274. [PMID: 36936052 PMCID: PMC10015121 DOI: 10.12688/f1000research.126227.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/31/2023] [Indexed: 02/10/2023] Open
Abstract
Background : Propolis is a natural resinous mixture produced by bees. It provides beneficial effects on human health in the treatment/management of many diseases. The present study was performed to demonstrate the anti- Acanthamoeba activity of ethanolic extracts of Propolis samples from Iran. The interactions of the compounds and essential proteins of Acanthamoeba were also visualized through docking simulation. Methods: The minimal inhibitory concentrations (MICs) of Propolis extract against Acanthamoeba trophozoites and cysts was determined in vitro. In addition, two-fold dilutions of each of agents were tested for encystment, excystment and adhesion inhibitions. Three major compounds of Propolis extract such as chrysin, tectochrysin and pinocembrin have been selected in molecular docking approach to predict the compounds that might be responsible for encystment, excystment and adhesion inhibitions of A. castellanii. Furthermore, to confirm the docking results, molecular dynamics (MD) simulations were also carried out for the most promising two ligand-pocket complexes from docking studies. Results : The minimal inhibitory concentrations (MICs) 62.5 and 125 µg/mL of the most active Propolis extract were assessed in trophozoites stage of Acanthamoeba castellanii ATCC30010 and ATCC50739, respectively. At concentrations lower than their MICs values (1/16 MIC), Propolis extract revealed inhibition of encystation. However, at 1/2 MIC, it showed a potential inhibition of excystation and anti-adhesion. The molecular docking and dynamic simulation revealed the potential capability of Pinocembrin to form hydrogen bonds with A. castellanii Sir2 family protein (AcSir2), an encystation protein of high relevance for this process in Acanthamoeba. Conclusions : The results provided a candidate for the development of therapeutic drugs against Acanthamoeba infection. In vivo experiments and clinical trials are necessary to support this claim.
Collapse
Affiliation(s)
- Imran Sama-ae
- Department of Medical Technology, School of Allied Health Sciences and Center of Excellence Research for Melioidosis and Microorganisms (CERMM), Walailak University, Nakhon Si Thammarat, Thailand
| | - Suthinee Sangkanu
- School of Allied Health Sciences, Southeast Asia Water Team (SEA Water Team) and World Union for Herbal Drug Discovery (WUHeDD), Walailak University, Nakhon Si Thammarat, Thailand
| | - Abolghasem Siyadatpanah
- Ferdows School of Paramedical and Health, Birjand University of Medical Sciences, Birjand, Iran
- Department of Microbiology, School of Medicine, Infectious Diseases Research Center, Gonabad University of Medical Sciences, Gonabad, Iran
| | - Roghayeh Norouzi
- Department of Pathobiology, Faculty of Veterinary Medicine, University of Tabriz, Tabriz, Iran
| | - Julalak Chuprom
- School of Allied Health Sciences, Southeast Asia Water Team (SEA Water Team) and World Union for Herbal Drug Discovery (WUHeDD), Walailak University, Nakhon Si Thammarat, Thailand
| | - Watcharapong Mitsuwan
- Akkhraratchakumari Veterinary College and Research Center of Excellence in Innovation of Essential Oil, Walailak University, Nakhon Si Thammarat, Thailand
| | - Sirirat Surinkaew
- Department of Medical Technology, School of Allied Health Sciences and Research Excellence Center for Innovation and Health Products (RECIHP), Walailak University, Nakhon Si Thammarat, Thailand
| | - Rachasak Boonhok
- Department of Medical Technology, School of Allied Health Sciences and Research Excellence Center for Innovation and Health Products (RECIHP), Walailak University, Nakhon Si Thammarat, Thailand
| | - Alok K. Paul
- School of Pharmacy and Pharmacology, University of Tasmania, TAS, Australia
| | - Tooba Mahboob
- School of Allied Health Sciences, Southeast Asia Water Team (SEA Water Team) and World Union for Herbal Drug Discovery (WUHeDD), Walailak University, Nakhon Si Thammarat, Thailand
| | - Najme Sadat Abtahi
- Department of Clinical Biochemistry, Faculty of Medicine International Campus, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Tajudeen O. Jimoh
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
- Department of Biochemistry, Faculty of Health Sciences, Islamic University in Uganda, Kampala, Uganda
| | - Sónia M.R. Oliveira
- CICECO-Aveiro Institute of Materials, University of Aveiro, Aveiro, Portugal
- Hunter Medical Research Institute, NSW, Australia
| | - Madhu Gupta
- Department of Pharmaceutics, Delhi Pharmaceutical Sciences and Research University, New Delhi, India
| | - Chea Sin
- Faculty of Pharmacy, University of Puthisastra, Phnom Penh, Cambodia
| | - Maria de Lourdes Pereira
- CICECO-Aveiro Institute of Materials, University of Aveiro, Aveiro, Portugal
- Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Polrat Wilairatana
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Christophe Wiart
- Institute for Tropical Biology & Conservation, University Malaysia Sabah, Sabah, Malaysia
| | - Mohammed Rahmatullah
- Department of Biotechnology & Genetic Engineering, University of Development Alternative, Dhaka, Bangladesh
| | - Karma G. Dolma
- Department of Microbiology, Sikkim Manipal Institute of Medical Sciences, Sikkim Manipal University, Sikkim, India
| | - Veeranoot Nissapatorn
- School of Allied Health Sciences, Southeast Asia Water Team (SEA Water Team) and World Union for Herbal Drug Discovery (WUHeDD), Walailak University, Nakhon Si Thammarat, Thailand
| |
Collapse
|
12
|
Banni GAHD, Nehmé R. Capillary electrophoresis for enzyme-based studies: Applications to lipases and kinases. J Chromatogr A 2021; 1661:462687. [PMID: 34864234 DOI: 10.1016/j.chroma.2021.462687] [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: 04/14/2021] [Revised: 11/05/2021] [Accepted: 11/14/2021] [Indexed: 10/19/2022]
Abstract
Capillary electrophoresis (CE) is a powerful technique continuously expanding into new application fields. One of these applications involves the study of enzymes, their catalytic activities and the alteration of this activity by specific ligands. In this review, two model enzymes, lipases and kinases, will be used since they differ substantially in their modes of action, reaction requirements and applications making them perfect subjects to demonstrate the advantages and limitations of CE-based enzymatic assays. Indeed, the ability to run CE in various operation modes and hyphenation to different detectors is essential for lipase-based studies. Additionally, the low sample consumption provided by CE promotes it as a promising technique to assay human and viral nucleoside kinases. Undeniably, these are rarely commercially available enzymes and must be frequently produced in the laboratory, a process which requires special sets of skills. CE-based lipase and kinase reactions can be performed outside the capillary (pre-capillary) where the reactants are mixed in a vial prior to their separation or, inside the capillary (in-capillary) where the reactants are mixed before the electrophoretic analysis. These enzyme-based applications of CE will be compared to those of liquid chromatography-based applications in terms of advantages and limitations. Binding assays based on affinity CE and the compelling microscale thermophoresis (MST) will be briefly presented as they allow a broad understanding of the molecular mechanism behind ligand binding and of the resulting modulation in activity.
Collapse
Affiliation(s)
- Ghassan Al Hamoui Dit Banni
- Institut de Chimie Organique et Analytique (ICOA), CNRS FR 2708 - UMR 7311, Université d'Orléans, Orléans 45067, France
| | - Reine Nehmé
- Institut de Chimie Organique et Analytique (ICOA), CNRS FR 2708 - UMR 7311, Université d'Orléans, Orléans 45067, France.
| |
Collapse
|
13
|
Das A, Yadav A, Gupta M, R P, Terse VL, Vishvakarma V, Singh S, Nandi T, Banerjee A, Mandal K, Gosavi S, Das R, Ainavarapu SRK, Maiti S. Rational Design of Protein-Specific Folding Modifiers. J Am Chem Soc 2021; 143:18766-18776. [PMID: 34724378 DOI: 10.1021/jacs.1c09611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein-folding can go wrong in vivo and in vitro, with significant consequences for the living organism and the pharmaceutical industry, respectively. Here we propose a design principle for small-peptide-based protein-specific folding modifiers. The principle is based on constructing a "xenonucleus", which is a prefolded peptide that mimics the folding nucleus of a protein. Using stopped-flow kinetics, NMR spectroscopy, Förster resonance energy transfer, single-molecule force measurements, and molecular dynamics simulations, we demonstrate that a xenonucleus can make the refolding of ubiquitin faster by 33 ± 5%, while variants of the same peptide have little or no effect. Our approach provides a novel method for constructing specific, genetically encodable folding catalysts for suitable proteins that have a well-defined contiguous folding nucleus.
Collapse
Affiliation(s)
- Anirban Das
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Anju Yadav
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Mona Gupta
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Purushotham R
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore 560065, India
| | - Vishram L Terse
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Vicky Vishvakarma
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Sameer Singh
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Hyderabad 500107, India
| | - Tathagata Nandi
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Arkadeep Banerjee
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Kalyaneswar Mandal
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Hyderabad 500107, India
| | - Shachi Gosavi
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Ranabir Das
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | | | - Sudipta Maiti
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| |
Collapse
|
14
|
Meena VK, Kumar V, Karalia S, Garima, Sundd M. Ellagic Acid Modulates Uninduced as well as Mutation and Metal-Induced Aggregation of α-Synuclein: Implications for Parkinson's Disease. ACS Chem Neurosci 2021; 12:3598-3614. [PMID: 34506119 DOI: 10.1021/acschemneuro.1c00317] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
α-Synuclein (αS) is an intrinsically disordered protein whose aggregation and deposition in Lewy bodies is involved in the progression of Parkinson's disease (PD) and other related disorders. The aggregation process of αS is also triggered by mutations like A53T and E46K in the SNCA gene and disruption in metal-ion homeostasis. Currently, there is no obviating therapy available in the market that could effectively prevent the progression of the disease. In this backdrop, there exists an emerging need to consider naturally occurring polyphenols and flavonoids as potential therapeutic agents against PD. In this study, we demonstrate the modulatory effect of ellagic acid (EA) against wild-type as well as mutation and metal-induced aggregation of αS. Thioflavin T (ThT) fluorescence assay suggests that EA acts on the nucleation phase of αS fibrillization, thereby increasing the lag phase from 21.33 ± 3.01 to 48.20 ± 5.05 h and reducing the fibrils growth rate from 4.60 ± 2.06 to 0.890 ± 0.36 h-1. 8-Anilino-1-naphthalene sulfonic acid (ANS), Congo red (CR), and intrinsic fluorescence studies indicate that the interaction of EA with αS facilitates the structural changes in the protein that lead to inhibition of fibril formation. Dynamic light scattering (DLS) and transmission electron microscopy (TEM) images illustrate that the size of fibrils diminishes up to 100 nm in the presence of EA. Dot blot and seeding experiments put forward that EA directs the αS aggregation toward off-pathway fibrillization. Our 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay deciphers the role of EA in minimizing the αS fibril-induced toxicity, thereupon leading to an increase in cell viability. Also, EA attenuates both mutations as well as metal-induced αS fibrillization and disaggregates the preexisting fibrils. Additionally, computational studies elucidate that EA preferentially interacts with the N-terminal and NAC domain of αS. Hence, this work reveals the aggregation inhibition mechanism of EA and provides considerable therapeutic interventions against PD and related disorders.
Collapse
Affiliation(s)
- Vinod Kumar Meena
- NMR-II Lab, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Vijay Kumar
- NMR-II Lab, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Shivani Karalia
- NMR-II Lab, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Garima
- NMR-II Lab, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Monica Sundd
- NMR-II Lab, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| |
Collapse
|
15
|
Bartels K, Lasitza‐Male T, Hofmann H, Löw C. Single-Molecule FRET of Membrane Transport Proteins. Chembiochem 2021; 22:2657-2671. [PMID: 33945656 PMCID: PMC8453700 DOI: 10.1002/cbic.202100106] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/03/2021] [Indexed: 12/31/2022]
Abstract
Uncovering the structure and function of biomolecules is a fundamental goal in structural biology. Membrane-embedded transport proteins are ubiquitous in all kingdoms of life. Despite structural flexibility, their mechanisms are typically studied by ensemble biochemical methods or by static high-resolution structures, which complicate a detailed understanding of their dynamics. Here, we review the recent progress of single molecule Förster Resonance Energy Transfer (smFRET) in determining mechanisms and timescales of substrate transport across membranes. These studies do not only demonstrate the versatility and suitability of state-of-the-art smFRET tools for studying membrane transport proteins but they also highlight the importance of membrane mimicking environments in preserving the function of these proteins. The current achievements advance our understanding of transport mechanisms and have the potential to facilitate future progress in drug design.
Collapse
Affiliation(s)
- Kim Bartels
- Centre for Structural Systems Biology (CSSB)DESY and European Molecular Biology Laboratory HamburgNotkestrasse 8522607HamburgGermany
| | - Tanya Lasitza‐Male
- Department of Structural BiologyWeizmann Institute of ScienceHerzl St. 2347610001RehovotIsrael
| | - Hagen Hofmann
- Department of Structural BiologyWeizmann Institute of ScienceHerzl St. 2347610001RehovotIsrael
| | - Christian Löw
- Centre for Structural Systems Biology (CSSB)DESY and European Molecular Biology Laboratory HamburgNotkestrasse 8522607HamburgGermany
| |
Collapse
|
16
|
Iljina M, Mazal H, Goloubinoff P, Riven I, Haran G. Entropic Inhibition: How the Activity of a AAA+ Machine Is Modulated by Its Substrate-Binding Domain. ACS Chem Biol 2021; 16:775-785. [PMID: 33739813 PMCID: PMC8056383 DOI: 10.1021/acschembio.1c00156] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
ClpB is a tightly regulated AAA+ disaggregation machine. Each ClpB molecule is composed of a flexibly attached N-terminal domain (NTD), an essential middle domain (MD) that activates the machine by tilting, and two nucleotide-binding domains. The NTD is not well-characterized structurally and is commonly considered to serve as a dispensable substrate-binding domain. Here, we use single-molecule FRET spectroscopy to directly monitor the real-time dynamics of ClpB's NTD and reveal its unexpected autoinhibitory function. We find that the NTD fluctuates on the microsecond time scale, and these dynamics result in steric hindrance that limits the conformational space of the MD to restrict its tilting. This leads to significantly inhibited ATPase and disaggregation activities of ClpB, an effect that is alleviated upon binding of a substrate protein or the cochaperone DnaK. This entropic inhibition mechanism, which is mediated by ultrafast motions of the NTD and is not dependent on any strong interactions, might be common in related ATP-dependent proteases and other multidomain proteins to ensure their fast and reversible activation.
Collapse
Affiliation(s)
- Marija Iljina
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Hisham Mazal
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Pierre Goloubinoff
- Department of Plant Molecular Biology, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Inbal Riven
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Gilad Haran
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 761001, Israel
| |
Collapse
|
17
|
From folding to function: complex macromolecular reactions unraveled one-by-one with optical tweezers. Essays Biochem 2021; 65:129-142. [PMID: 33438724 DOI: 10.1042/ebc20200024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/08/2020] [Accepted: 12/11/2020] [Indexed: 12/13/2022]
Abstract
Single-molecule manipulation with optical tweezers has uncovered macromolecular behaviour hidden to other experimental techniques. Recent instrumental improvements have made it possible to expand the range of systems accessible to optical tweezers. Beyond focusing on the folding and structural changes of isolated single molecules, optical tweezers studies have evolved into unraveling the basic principles of complex molecular processes such as co-translational folding on the ribosome, kinase activation dynamics, ligand-receptor binding, chaperone-assisted protein folding, and even dynamics of intrinsically disordered proteins (IDPs). In this mini-review, we illustrate the methodological principles of optical tweezers before highlighting recent advances in studying complex protein conformational dynamics - from protein synthesis to physiological function - as well as emerging future issues that are beginning to be addressed with novel approaches.
Collapse
|
18
|
Lerner E, Barth A, Hendrix J, Ambrose B, Birkedal V, Blanchard SC, Börner R, Sung Chung H, Cordes T, Craggs TD, Deniz AA, Diao J, Fei J, Gonzalez RL, Gopich IV, Ha T, Hanke CA, Haran G, Hatzakis NS, Hohng S, Hong SC, Hugel T, Ingargiola A, Joo C, Kapanidis AN, Kim HD, Laurence T, Lee NK, Lee TH, Lemke EA, Margeat E, Michaelis J, Michalet X, Myong S, Nettels D, Peulen TO, Ploetz E, Razvag Y, Robb NC, Schuler B, Soleimaninejad H, Tang C, Vafabakhsh R, Lamb DC, Seidel CAM, Weiss S. FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices. eLife 2021; 10:e60416. [PMID: 33779550 PMCID: PMC8007216 DOI: 10.7554/elife.60416] [Citation(s) in RCA: 135] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 02/09/2021] [Indexed: 12/18/2022] Open
Abstract
Single-molecule FRET (smFRET) has become a mainstream technique for studying biomolecular structural dynamics. The rapid and wide adoption of smFRET experiments by an ever-increasing number of groups has generated significant progress in sample preparation, measurement procedures, data analysis, algorithms and documentation. Several labs that employ smFRET approaches have joined forces to inform the smFRET community about streamlining how to perform experiments and analyze results for obtaining quantitative information on biomolecular structure and dynamics. The recent efforts include blind tests to assess the accuracy and the precision of smFRET experiments among different labs using various procedures. These multi-lab studies have led to the development of smFRET procedures and documentation, which are important when submitting entries into the archiving system for integrative structure models, PDB-Dev. This position paper describes the current 'state of the art' from different perspectives, points to unresolved methodological issues for quantitative structural studies, provides a set of 'soft recommendations' about which an emerging consensus exists, and lists openly available resources for newcomers and seasoned practitioners. To make further progress, we strongly encourage 'open science' practices.
Collapse
Affiliation(s)
- Eitan Lerner
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, and The Center for Nanoscience and Nanotechnology, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of JerusalemJerusalemIsrael
| | - Anders Barth
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-UniversitätDüsseldorfGermany
| | - Jelle Hendrix
- Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre and Biomedical Research Institute (BIOMED), Hasselt UniversityDiepenbeekBelgium
| | - Benjamin Ambrose
- Department of Chemistry, University of SheffieldSheffieldUnited Kingdom
| | - Victoria Birkedal
- Department of Chemistry and iNANO center, Aarhus UniversityAarhusDenmark
| | - Scott C Blanchard
- Department of Structural Biology, St. Jude Children's Research HospitalMemphisUnited States
| | - Richard Börner
- Laserinstitut HS Mittweida, University of Applied Science MittweidaMittweidaGermany
| | - Hoi Sung Chung
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesdaUnited States
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität MünchenPlanegg-MartinsriedGermany
| | - Timothy D Craggs
- Department of Chemistry, University of SheffieldSheffieldUnited Kingdom
| | - Ashok A Deniz
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Jiajie Diao
- Department of Cancer Biology, University of Cincinnati School of MedicineCincinnatiUnited States
| | - Jingyi Fei
- Department of Biochemistry and Molecular Biology and The Institute for Biophysical Dynamics, University of ChicagoChicagoUnited States
| | - Ruben L Gonzalez
- Department of Chemistry, Columbia UniversityNew YorkUnited States
| | - Irina V Gopich
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesdaUnited States
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Howard Hughes Medical InstituteBaltimoreUnited States
| | - Christian A Hanke
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-UniversitätDüsseldorfGermany
| | - Gilad Haran
- Department of Chemical and Biological Physics, Weizmann Institute of ScienceRehovotIsrael
| | - Nikos S Hatzakis
- Department of Chemistry & Nanoscience Centre, University of CopenhagenCopenhagenDenmark
- Denmark Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of CopenhagenCopenhagenDenmark
| | - Sungchul Hohng
- Department of Physics and Astronomy, and Institute of Applied Physics, Seoul National UniversitySeoulRepublic of Korea
| | - Seok-Cheol Hong
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science and Department of Physics, Korea UniversitySeoulRepublic of Korea
| | - Thorsten Hugel
- Institute of Physical Chemistry and Signalling Research Centres BIOSS and CIBSS, University of FreiburgFreiburgGermany
| | - Antonino Ingargiola
- Department of Chemistry and Biochemistry, and Department of Physiology, University of California, Los AngelesLos AngelesUnited States
| | - Chirlmin Joo
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of TechnologyDelftNetherlands
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of OxfordOxfordUnited Kingdom
| | - Harold D Kim
- School of Physics, Georgia Institute of TechnologyAtlantaUnited States
| | - Ted Laurence
- Physical and Life Sciences Directorate, Lawrence Livermore National LaboratoryLivermoreUnited States
| | - Nam Ki Lee
- School of Chemistry, Seoul National UniversitySeoulRepublic of Korea
| | - Tae-Hee Lee
- Department of Chemistry, Pennsylvania State UniversityUniversity ParkUnited States
| | - Edward A Lemke
- Departments of Biology and Chemistry, Johannes Gutenberg UniversityMainzGermany
- Institute of Molecular Biology (IMB)MainzGermany
| | - Emmanuel Margeat
- Centre de Biologie Structurale (CBS), CNRS, INSERM, Universitié de MontpellierMontpellierFrance
| | | | - Xavier Michalet
- Department of Chemistry and Biochemistry, and Department of Physiology, University of California, Los AngelesLos AngelesUnited States
| | - Sua Myong
- Department of Biophysics, Johns Hopkins UniversityBaltimoreUnited States
| | - Daniel Nettels
- Department of Biochemistry and Department of Physics, University of ZurichZurichSwitzerland
| | - Thomas-Otavio Peulen
- Department of Bioengineering and Therapeutic Sciences, University of California, San FranciscoSan FranciscoUnited States
| | - Evelyn Ploetz
- Physical Chemistry, Department of Chemistry, Center for Nanoscience (CeNS), Center for Integrated Protein Science Munich (CIPSM) and Nanosystems Initiative Munich (NIM), Ludwig-Maximilians-UniversitätMünchenGermany
| | - Yair Razvag
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, and The Center for Nanoscience and Nanotechnology, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of JerusalemJerusalemIsrael
| | - Nicole C Robb
- Warwick Medical School, University of WarwickCoventryUnited Kingdom
| | - Benjamin Schuler
- Department of Biochemistry and Department of Physics, University of ZurichZurichSwitzerland
| | - Hamid Soleimaninejad
- Biological Optical Microscopy Platform (BOMP), University of MelbourneParkvilleAustralia
| | - Chun Tang
- College of Chemistry and Molecular Engineering, PKU-Tsinghua Center for Life Sciences, Beijing National Laboratory for Molecular Sciences, Peking UniversityBeijingChina
| | - Reza Vafabakhsh
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Don C Lamb
- Physical Chemistry, Department of Chemistry, Center for Nanoscience (CeNS), Center for Integrated Protein Science Munich (CIPSM) and Nanosystems Initiative Munich (NIM), Ludwig-Maximilians-UniversitätMünchenGermany
| | - Claus AM Seidel
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-UniversitätDüsseldorfGermany
| | - Shimon Weiss
- Department of Chemistry and Biochemistry, and Department of Physiology, University of California, Los AngelesLos AngelesUnited States
- Department of Physiology, CaliforniaNanoSystems Institute, University of California, Los AngelesLos AngelesUnited States
| |
Collapse
|
19
|
Gupta M, Venkatramani R, Ainavarapu SRK. Role of Ligand Binding Site in Modulating the Mechanical Stability of Proteins with β-Grasp Fold. J Phys Chem B 2021; 125:1009-1019. [PMID: 33492970 DOI: 10.1021/acs.jpcb.0c08085] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Despite many studies on ligand-modulated protein mechanics, a comparative analysis of the role of ligand binding site on any specific protein fold is yet to be made. In this study, we explore the role of ligand binding site on the mechanical properties of β-grasp fold proteins, namely, ubiquitin and small ubiquitin related modifier 1 (SUMO1). The terminal segments directly connected through hydrogen bonds constitute the β-clamp geometry (or mechanical clamp), which confers high mechanical resilience to the β-grasp fold. Here, we study ubiquitin complexed with CUE2-1, a ubiquitin-binding domain (UBD) from yeast endonuclease protein Cue2, using a combination of single-molecule force spectroscopy (SMFS) and steered molecular dynamics (SMD) simulations. Our study reveals that CUE2-1 does not alter the mechanical properties of ubiquitin, despite directly interacting with its β-clamp. To explore the role of ligand binding site, we compare the mechanical properties of the ubiquitin/CUE2-1 complex with that of previously studied SUMO1/S12, another β-grasp protein complex, using SMD simulations. Simulations on the SUMO1/S12 complex corroborate previous experimentally observed enhancement in the mechanical stability of SUMO1, even though S12 binds away from the β-clamp. Differences in ligand binding-induced structural impact at the transition state of the two complexes explain the differences in ligand modulated protein mechanics. Contrary to previous reports, our study demonstrates that direct binding of ligands to the mechanical clamp does not necessarily alter the mechanical stability of β-grasp fold proteins. Rather, binding interactions away from the clamp can reinforce protein stability provided by the β-grasp fold. Our study highlights the importance of binding site and binding modes of ligands in modulating the mechanical stability of β-grasp fold proteins.
Collapse
Affiliation(s)
- Mona Gupta
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Dr Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Ravindra Venkatramani
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Dr Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Sri Rama Koti Ainavarapu
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Dr Homi Bhabha Road, Colaba, Mumbai 400005, India
| |
Collapse
|
20
|
Thangavel N, Al Bratty M, Al Hazmi HA, Najmi A, Ali Alaqi RO. Molecular Docking and Molecular Dynamics Aided Virtual Search of OliveNet™ Directory for Secoiridoids to Combat SARS-CoV-2 Infection and Associated Hyperinflammatory Responses. Front Mol Biosci 2021; 7:627767. [PMID: 33490110 PMCID: PMC7817976 DOI: 10.3389/fmolb.2020.627767] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 12/02/2020] [Indexed: 12/11/2022] Open
Abstract
Molecular docking and molecular dynamics aided virtual search of OliveNet™ directory identified potential secoiridoids that combat SARS-CoV-2 entry, replication, and associated hyperinflammatory responses. OliveNet™ is an active directory of phytochemicals obtained from different parts of the olive tree, Olea europaea (Oleaceae). Olive oil, olive fruits containing phenolics, known for their health benefits, are indispensable in the Mediterranean and Arabian diets. Secoiridoids is the largest group of olive phenols and is exclusive to the olive fruits. Functional food like olive fruits could help prevent and alleviate viral disease at an affordable cost. A systematized virtual search of 932 conformers of 78 secoiridoids utilizing Autodock Vina, followed by precision docking using Idock and Smina indicated that Nüzhenide oleoside (NZO), Oleuropein dimer (OED), and Dihydro oleuropein (DHO) blocked the SARS-CoV-2 spike (S) protein-ACE-2 interface; Demethyloleuropein (DMO), Neo-nüzhenide (NNZ), and Nüzhenide (NZE) blocked the SARS-CoV-2 main protease (Mpro). Molecular dynamics (MD) simulation of the NZO-S-protein-ACE-2 complex by Desmond revealed stability during 50 ns. RMSD of the NZO-S-protein-ACE-2 complex converged at 2.1 Å after 20 ns. During MD, the interaction fractions confirmed multiple interactions of NZO with Lys417, a crucial residue for inhibition of S protein. MD of DMO-Mpro complex proved its stability as the RMSD converged at 1.6 Å. Analysis of interactions during MD confirmed the interaction of Cys145 of Mpro with DMO and, thus, its inhibition. The docking predicted IC50 of NZO and DMO was 11.58 and 6.44 μM, respectively. Molecular docking and dynamics of inhibition of the S protein and Mpro by NZO and DMO correlated well. Docking of the six-hit secoiridoids to IL1R, IL6R, and TNFR1, the receptors of inflammatory cytokines IL1β, IL6, and TNFα, revealed the anti-inflammatory potential except for DHO. Due to intricate structures, the secoiridoids violated Lipinski's rule of five. However, the drug scores of secoiridoids supported their use as drugs. The ADMET predictions implied that the secoiridoids are non-toxic and pose low oral absorption. Secoiridoids need further optimization and are a suitable lead for the discovery of anti-SARS-CoV-2 therapeutics. For the moment, olive secoiridoids presents an accessible mode of prevention and therapy of SARS-CoV-2 infection.
Collapse
Affiliation(s)
- Neelaveni Thangavel
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Jazan University, Jazan, Saudi Arabia
| | | | | | | | | |
Collapse
|
21
|
Brylski O, Ebbinghaus S, Mueller JW. Melting Down Protein Stability: PAPS Synthase 2 in Patients and in a Cellular Environment. Front Mol Biosci 2019; 6:31. [PMID: 31131283 PMCID: PMC6509946 DOI: 10.3389/fmolb.2019.00031] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 04/15/2019] [Indexed: 12/17/2022] Open
Abstract
Within the crowded and complex environment of the cell, a protein experiences stabilizing excluded-volume effects and destabilizing quinary interactions with other proteins. Which of these prevail, needs to be determined on a case-by-case basis. PAPS synthases are dimeric and bifunctional enzymes, providing activated sulfate in the form of 3′-phosphoadenosine-5′-phosphosulfate (PAPS) for sulfation reactions. The human PAPS synthases PAPSS1 and PAPSS2 differ significantly in their protein stability as PAPSS2 is a naturally fragile protein. PAPS synthases bind a series of nucleotide ligands and some of them markedly stabilize these proteins. PAPS synthases are of biomedical relevance as destabilizing point mutations give rise to several pathologies. Genetic defects in PAPSS2 have been linked to bone and cartilage malformations as well as a steroid sulfation defect. All this makes PAPS synthases ideal to study protein unfolding, ligand binding, and the stabilizing and destabilizing factors in their cellular environment. This review provides an overview on current concepts of protein folding and stability and links this with our current understanding of the different disease mechanisms of PAPSS2-related pathologies with perspectives for future research and application.
Collapse
Affiliation(s)
- Oliver Brylski
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Simon Ebbinghaus
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Jonathan W Mueller
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom.,Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, United Kingdom
| |
Collapse
|
22
|
Tunable microsecond dynamics of an allosteric switch regulate the activity of a AAA+ disaggregation machine. Nat Commun 2019; 10:1438. [PMID: 30926805 PMCID: PMC6440998 DOI: 10.1038/s41467-019-09474-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 03/14/2019] [Indexed: 12/13/2022] Open
Abstract
Large protein machines are tightly regulated through allosteric communication channels. Here we demonstrate the involvement of ultrafast conformational dynamics in allosteric regulation of ClpB, a hexameric AAA+ machine that rescues aggregated proteins. Each subunit of ClpB contains a unique coiled-coil structure, the middle domain (M domain), proposed as a control element that binds the co-chaperone DnaK. Using single-molecule FRET spectroscopy, we probe the M domain during the chaperone cycle and find it to jump on the microsecond time scale between two states, whose structures are determined. The M-domain jumps are much faster than the overall activity of ClpB, making it an effectively continuous, tunable switch. Indeed, a series of allosteric interactions are found to modulate the dynamics, including binding of nucleotides, DnaK and protein substrates. This mode of dynamic control enables fast cellular adaptation and may be a general mechanism for the regulation of cellular machineries. Large protein machines are tightly regulated through allosteric communication channels. Here authors use single-molecule FRET and demonstrate the involvement of ultrafast conformational dynamics in the allosteric regulation of ClpB, a hexameric AAA+ machine that rescues aggregated proteins.
Collapse
|
23
|
The Svedberg Lecture 2017. From nano to micro: the huge dynamic range of the analytical ultracentrifuge for characterising the sizes, shapes and interactions of molecules and assemblies in Biochemistry and Polymer Science. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2018; 47:697-707. [PMID: 30056489 PMCID: PMC6182603 DOI: 10.1007/s00249-018-1321-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 04/25/2018] [Accepted: 07/06/2018] [Indexed: 12/19/2022]
Abstract
The analytical ultracentrifuge (AUC) invented by T. Svedberg has now become an extremely versatile and diverse tool in Biochemistry and Polymer Science for the characterisation of the sizes, shapes and interactions of particles ranging in size from a few nanometres to tens of microns, or in molecular weight, M (molar mass) terms from a few hundred daltons to hundreds of megadaltons. We illustrate this diversity by reviewing recent work on (1) small lignin-like isoeugenols of M ~ 0.4–0.9 kDa for archaeological wood conservation, (2) protein-like association of a functional amino-cellulose M = 3.25 kDa, (3) a small glycopeptide antibiotic (M ~ 1.5 kDa) and its association with a protein involved in antibiotic resistance (M ~ 47 kDa), (4) tetanus toxoid protein TTP (M ~ 150 kDa) and (5) the incorporation of TTP into two huge glycoconjugates considered in glycovaccine development with molecular weight species in a broad distribution appearing to reach 100 MDa. In illustrating the diversity, we will highlight developments in hydrodynamic analysis which have made the AUC such an exciting and important instrument, and point to a potential future development for extending its capability to highly concentrated systems.
Collapse
|
24
|
Modi T, Huihui J, Ghosh K, Ozkan SB. Ancient thioredoxins evolved to modern-day stability-function requirement by altering native state ensemble. Philos Trans R Soc Lond B Biol Sci 2018; 373:20170184. [PMID: 29735738 PMCID: PMC5941179 DOI: 10.1098/rstb.2017.0184] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/20/2018] [Indexed: 02/06/2023] Open
Abstract
Thioredoxins (THRXs)-small globular proteins that reduce other proteins-are ubiquitous in all forms of life, from Archaea to mammals. Although ancestral thioredoxins share sequential and structural similarity with the modern-day (extant) homologues, they exhibit significantly different functional activity and stability. We investigate this puzzle by comparative studies of their (ancient and modern-day THRXs') native state ensemble, as quantified by the dynamic flexibility index (DFI), a metric for the relative resilience of an amino acid to perturbations in the rest of the protein. Clustering proteins using DFI profiles strongly resemble an alternative classification scheme based on their activity and stability. The DFI profiles of the extant proteins are substantially different around the α3, α4 helices and catalytic regions. Likewise, allosteric coupling of the active site with the rest of the protein is different between ancient and extant THRXs, possibly explaining the decreased catalytic activity at low pH with evolution. At a global level, we note that the population of low-flexibility (called hinges) and high-flexibility sites increases with evolution. The heterogeneity (quantified by the variance) in DFI distribution increases with the decrease in the melting temperature typically associated with the evolution of ancient proteins to their modern-day counterparts.This article is part of a discussion meeting issue 'Allostery and molecular machines'.
Collapse
Affiliation(s)
- Tushar Modi
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, AZ 85281, USA
| | - Jonathan Huihui
- Department of Physics and Astronomy, University of Denver, Denver, CO 80209, USA
| | - Kingshuk Ghosh
- Department of Physics and Astronomy, University of Denver, Denver, CO 80209, USA
| | - S Banu Ozkan
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, AZ 85281, USA
| |
Collapse
|
25
|
Direct observation of ultrafast large-scale dynamics of an enzyme under turnover conditions. Proc Natl Acad Sci U S A 2018. [PMID: 29531052 PMCID: PMC5879700 DOI: 10.1073/pnas.1720448115] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The potential effect of conformational dynamics of enzymes on their chemical steps has been intensely debated recently. We use single-molecule FRET experiments on adenylate kinase (AK) to shed new light on this question. AK closes its domains to bring its two substrate close together for reaction. We show that domain closure takes only microseconds to complete, which is two orders of magnitude faster than the chemical reaction. Nevertheless, active-site mutants that reduce the rate of domain closure also reduce the reaction rate, suggesting a connection between the two phenomena. We propose that ultrafast domain closure is used by enzymes as a mechanism to optimize mutual orientation of substrates, a novel mode of coupling between conformational dynamics and catalysis. The functional cycle of many proteins involves large-scale motions of domains and subunits. The relation between conformational dynamics and the chemical steps of enzymes remains under debate. Here we show that in the presence of substrates, domain motions of an enzyme can take place on the microsecond time scale, yet exert influence on the much-slower chemical step. We study the domain closure reaction of the enzyme adenylate kinase from Escherichia coli while in action (i.e., under turnover conditions), using single-molecule FRET spectroscopy. We find that substrate binding increases dramatically domain closing and opening times, making them as short as ∼15 and ∼45 µs, respectively. These large-scale conformational dynamics are likely the fastest measured to date, and are ∼100–200 times faster than the enzymatic turnover rate. Some active-site mutants are shown to fully or partially prevent the substrate-induced increase in domain closure times, while at the same time they also reduce enzymatic activity, establishing a clear connection between the two phenomena, despite their disparate time scales. Based on these surprising observations, we propose a paradigm for the mode of action of enzymes, in which numerous cycles of conformational rearrangement are required to find a mutual orientation of substrates that is optimal for the chemical reaction.
Collapse
|