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Nagani A, Shah M, Patel S, Patel H, Parikh V, Patel A, Patel S, Patel K, Parmar H, Bhimani B, Yadav MR. Unveiling piperazine-quinoline hybrids as potential multi-target directed anti-Alzheimer's agents: design, synthesis and biological evaluation. Mol Divers 2024:10.1007/s11030-024-10927-4. [PMID: 38990393 DOI: 10.1007/s11030-024-10927-4] [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: 03/14/2024] [Accepted: 07/02/2024] [Indexed: 07/12/2024]
Abstract
Multi-target directed ligands (MTDLs) have recently been popularized due to their outstanding efficacy in combating the complicated features of Alzheimer's disease. This study details the synthesis of piperazine-quinoline-based MTDLs through a multicomponent Petasis reaction, targeting multiple factors such as AChE, BuChE, metal chelation to restore metal dyshomeostasis, and antioxidant activity. Some of the synthesized compounds exhibited notable inhibitory activity against AChE and BuChE enzymes at specific concentrations. Among the synthesized compounds compound (95) containing a 4-chloroaniline moiety and a 4-methoxybenzyl group displayed the most promising inhibitory activities against AChE (IC50 3.013 µM) and BuChE (IC50 = 3.144 µM). Compound (83) featuring 2-methoxyaniline and 4-fluorobenzyl substituents, exhibited the highest BuChE inhibition (IC50 1.888 µM). Notably, compound (79) demonstrated 93-times higher selectivity for BuChE over AChE. Molecular docking and molecular dynamics simulations were also performed to explore the binding modes and stability of these compounds with the AChE amd BuChE proteins. Further, kinetics study was performed against AChE for comounds (83 and 95) which indicated mixed inhibition of the enzyme by these compounds, Amongs the synthesized compounds, nine compounds were assessed for their antioxidant activity, displaying significant antioxidant properties with IC50 values ranging from 156 µM to 310 µM. Moreover, all the compounds demonstrated metal chelating tendency with Cu+2, Zn+2, Fe+2, Fe+3 and Al+3. This study provides insights into the design of novel MTDLs, highlighting compound (95) as a potential candidate for combating Alzheimer's disease.
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Affiliation(s)
- Afzal Nagani
- Parul Institute of Pharmacy, Parul University, Vadodara, Gujarat, India
- Research and Development Cell, Parul University, Vadodara, Gujarat, India
| | - Moksh Shah
- Parul Institute of Pharmacy, Parul University, Vadodara, Gujarat, India
| | - Salman Patel
- Parul Institute of Pharmacy, Parul University, Vadodara, Gujarat, India
| | - Harnisha Patel
- Parul Institute of Pharmacy, Parul University, Vadodara, Gujarat, India
| | - Vruti Parikh
- Parul Institute of Pharmacy, Parul University, Vadodara, Gujarat, India
| | - Ashish Patel
- Ramanbhai Patel College of Pharmacy, Charotar University of Science and Technology, CHARUSAT Campus, Changa, Anand, Gujarat, India
| | - Sagar Patel
- Sunnybrook Research Institute, Sunnybrook Health Science Centre, University of Toronto, Toronto, ON, Canada
| | - Kirti Patel
- Faculty of Pharmacy, The M.S University of Baroda, Vadodara, Gujarat, India
| | - Hardik Parmar
- Faculty of Pharmacy, The M.S University of Baroda, Vadodara, Gujarat, India
| | | | - Mange Ram Yadav
- Research and Development Cell, Parul University, Vadodara, Gujarat, India.
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Bettadj FZY, Benchouk W. Computer-aided analysis for identification of novel analogues of ketoprofen based on molecular docking, ADMET, drug-likeness and DFT studies for the treatment of inflammation. J Biomol Struct Dyn 2023; 41:9915-9930. [PMID: 36444967 DOI: 10.1080/07391102.2022.2148750] [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: 08/11/2022] [Accepted: 11/12/2022] [Indexed: 11/30/2022]
Abstract
Computer-based drug design is increasingly used in strategies for discovering new molecules for therapeutic purposes. The targeted drug is ketoprofen (KTP), which belongs to the family of non-steroidal anti-inflammatory drugs, which are widely used for the treatment of pain, fever, inflammation and certain types of cancers. In an attempt to rationalize the search for 72 new potential anti-inflammatory compounds on the COX-2 enzyme, we carried out an in silico protocol that successfully combines molecular docking towards COX-2 receptor (5F1A), ADMET pharmacokinetic parameters, drug-likeness rules and molecular electrostatic potential (MEP). It was found that six of the compounds analyzed satisfy with the associated values to physico-chemical properties as key evaluation parameters for the drug-likeness and demonstrate a hydrophobic character which makes their solubility in aqueous media difficult and easy in lipids. All the compounds presented good ADMET profile and they showed an interaction with the amino acids responsible for anti-inflammatory activity of the COX-2 isoenzyme. The calculation of the MEP of the six analogues reveals new preferential sites involving the formation of new bonds. Consequently, this result allowed us to understand the origin of the potential increase in the anti-inflammatory activity of the candidates. Finally, it was obtained that six compounds have a binding mode, binding energy, and stability in the active site of COX-2 like the reference drug ketoprofen, suggesting that these compounds could become a powerful candidate in the inhibition of the COX-2 enzyme.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Fatima Zohra Yasmine Bettadj
- Laboratory of Applied Thermodynamics and Molecular Modeling, Department of Chemistry, Faculty of Science, University of Tlemcen, Tlemcen, Algeria
| | - Wafaa Benchouk
- Laboratory of Applied Thermodynamics and Molecular Modeling, Department of Chemistry, Faculty of Science, University of Tlemcen, Tlemcen, Algeria
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Kęska P, Stadnik J, Łupawka A, Michalska A. Novel α-Glucosidase Inhibitory Peptides Identified In Silico from Dry-Cured Pork Loins with Probiotics through Peptidomic and Molecular Docking Analysis. Nutrients 2023; 15:3539. [PMID: 37630730 PMCID: PMC10460020 DOI: 10.3390/nu15163539] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 08/09/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
Diabetes mellitus is a serious metabolic disorder characterized by abnormal blood glucose levels in the body. The development of therapeutic strategies for restoring and maintaining blood glucose homeostasis is still in progress. Synthetic alpha-amylase and alpha-glucosidase inhibitors can improve blood glucose control in diabetic patients by effectively reducing the risk of postprandial hyperglycemia. Peptides of natural origin are promising compounds that can serve as alpha-glucosidase inhibitors in the treatment of type 2 diabetes. Potential alpha-glucosidase-inhibiting peptides obtained from aqueous and saline extracts from dry-cured pork loins inoculated with probiotic LAB were evaluated using in vitro and in silico methods. To identify the peptide sequences, liquid chromatography-mass spectrometry was used. For this purpose, in silico calculation methods were used, and the occurrence of bioactive fragments in the protein followed the ADMET approach. The most promising sequences were molecularly docked to test their interaction with the human alpha-glycosidase molecule (PDB ID: 5NN8). The docking studies proved that oligopeptides VATPPPPPPPK, DIPPPPM, TPPPPPPG, and TPPPPPPPK obtained by hydrolysis of proteins from ripening dry-cured pork loins showed the potential to bind to the human alpha-glucosidase molecule and may act effectively as a potential antidiabetic agent.
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Affiliation(s)
| | - Joanna Stadnik
- Department of Animal Food Technology, Faculty of Food Science and Biotechnology, University of Life Sciences in Lublin, Skromna 8, 20-704 Lublin, Poland
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Guzmán-López EG, Reina M, Hernández-Ayala LF, Galano A. Rational Design of Multifunctional Ferulic Acid Derivatives Aimed for Alzheimer's and Parkinson's Diseases. Antioxidants (Basel) 2023; 12:1256. [PMID: 37371986 DOI: 10.3390/antiox12061256] [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: 04/29/2023] [Revised: 05/31/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
Ferulic acid has numerous beneficial effects on human health, which are frequently attributed to its antioxidant behavior. In this report, many of them are reviewed, and 185 new ferulic acid derivatives are computationally designed using the CADMA-Chem protocol. Consequently, their chemical space was sampled and evaluated. To that purpose, selection and elimination scores were used, which are built from a set of descriptors accounting for ADME properties, toxicity, and synthetic accessibility. After the first screening, 12 derivatives were selected and further investigated. Their potential role as antioxidants was predicted from reactivity indexes directly related to the formal hydrogen atom transfer and the single electron transfer mechanisms. The best performing molecules were identified by comparisons with the parent molecule and two references: Trolox and α-tocopherol. Their potential as polygenic neuroprotectors was investigated through the interactions with enzymes directly related to the etiologies of Parkinson's and Alzheimer's diseases. These enzymes are acetylcholinesterase, catechol-O-methyltransferase, and monoamine oxidase B. Based on the obtained results, the most promising candidates (FA-26, FA-118, and FA-138) are proposed as multifunctional antioxidants with potential neuroprotective effects. The findings derived from this investigation are encouraging and might promote further investigations on these molecules.
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Affiliation(s)
- Eduardo Gabriel Guzmán-López
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, Av. Ferrocarril San Rafael Atlixco 186, Col. Leyes de Reforma 1A Sección, Alcaldía Iztapalapa, Mexico City 09310, Mexico
| | - Miguel Reina
- Departamento de Química Inorgánica y Nuclear, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Luis Felipe Hernández-Ayala
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, Av. Ferrocarril San Rafael Atlixco 186, Col. Leyes de Reforma 1A Sección, Alcaldía Iztapalapa, Mexico City 09310, Mexico
| | - Annia Galano
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, Av. Ferrocarril San Rafael Atlixco 186, Col. Leyes de Reforma 1A Sección, Alcaldía Iztapalapa, Mexico City 09310, Mexico
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Bioinformatics identification and molecular mechanism of angiotensin-converting enzyme and dipeptidyl peptidase-IV inhibitory peptides from in silico digest of Crassostrea gigas. JOURNAL OF FOOD MEASUREMENT AND CHARACTERIZATION 2022. [DOI: 10.1007/s11694-022-01548-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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Kelutur FJ, Saptarini NM, Mustarichie R, Kurnia D. Molecular Docking of the Terpenes in Gorgonian Corals to COX-2 and
iNOS Enzymes as Anti-Inflammatory. LETT DRUG DES DISCOV 2022. [DOI: 10.2174/1570180819666211227162950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Because the inflammatory pathway is triggered by the enzymes cyclooxygenase-
2 (COX-2) and inducible nitric oxide synthase (iNOS), inhibitors, such as nonsteroidal anti-inflammatory
drugs (NSAIDs), are needed, although these have side effects. Therefore, the discovery and development
of natural medicine as a lead compound are needed. The gorgonian corals have been reported to contain
cyclic diterpenes with anti-inflammatory activities. The specific anti-inflammatory inhibitor potential has
not been reported regarding these secondary metabolites, whether in COX-2 or iNOS. Thus, the in silico
method is the right alternative.
Objective:
This study aimed to determine the potency of fifteen terpenes of the various gorgonian corals
to COX-2 and iNOS enzymes as an anti-inflammatory.
Methods:
Molecular docking was performed using ChemDraw Ultra 12.0, Chem3D Pro 12.0, Biovia
Discovery Studio 2016 Client®, Autodock Tools 4.2, prediction pharmacokinetics (Pre-ADMET), and
oral administration (Lipinski rule of five).
Results:
Potential terpenes based on ΔG (kcal/mol) and Ki (nM) to COX-2 were gyrosanol B (-10,32;
27,15), gyrosanol A (-10,20; 33,57), echinolabdane A (-9,81; 64,76). Only nine terpenes were specific to
COX-2 active sites, while for iNOS were palmonine F (-7.76; 2070), briarenol C (-7.55; 2910), and all
test compounds binding to the iNOS active sites. Pre-ADMET prediction obtained that HIA was very
excellent (70–100%), Caco-2 had moderate permeability (4–70 nm sec-1), and PPB had strong binding (>
90%). Eight terpenes qualified for the Lipinski rule of five.
Conclusion:
iNOS was a specific target for terpenes based on the free energy of binding (ΔG).
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Affiliation(s)
- Faruk Jayanto Kelutur
- Department of Pharmaceutical Analysis and Medicinal Chemistry, Faculty of Pharmacy, Universitas Padjadjaran,
West Java, Indonesia
| | - Nyi Mekar Saptarini
- Department of Pharmaceutical Analysis and Medicinal Chemistry, Faculty of Pharmacy, Universitas Padjadjaran,
West Java, Indonesia
| | - Resmi Mustarichie
- Department of Pharmaceutical Analysis and Medicinal Chemistry, Faculty of Pharmacy, Universitas Padjadjaran,
West Java, Indonesia
| | - Dikdik Kurnia
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran,
West Java, Indonesia
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Screening of Potential Breast Cancer Inhibitors through Molecular Docking and Molecular Dynamics Simulation. BIOMED RESEARCH INTERNATIONAL 2022; 2022:3338549. [PMID: 35800218 PMCID: PMC9256436 DOI: 10.1155/2022/3338549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/25/2022] [Accepted: 06/06/2022] [Indexed: 11/17/2022]
Abstract
Cyclooxygenase-2 (COX-2) is a key enzyme involved in overexpression in several human cancerous diseases including breast cancer. By performing efficient virtual screening in a series of active molecules or compounds from the Maybridge, NCI (National Cancer Institute), and Enamine databases, potential identification of COX-2 inhibitors could lead to new prognostic strategies in the treatment of breast cancer. Based on a 50% structural similitude, compounds were chosen as the inductive model of COX-2 inhibitions from these databases. Selected compounds were filtered and tested with Lipinski’s rule of five followed by absorption, distribution, metabolism, and excretion (ADME) properties. Subsequently, molecular docking was performed to achieve accuracy in screening and also to find an interactive mechanism between hit compounds with their respective binding sites. Simultaneously, molecular simulations of top-scored compounds were selected and coded such as Maybridge_55417, NCI_30552, and Enamine_62410. Chosen compounds were analyzed and interpreted with COX-2 affinity. Results endorsed that hydrophobic affinity and optimum hydrogen bonds were the forces driven in the interactive mechanism of in silico hits compounds with COX-2 and can be used as efficient alternative therapeutic agents targeting deleterious breast cancer. With these in silico findings, compounds identified may prevent the action of the COX-2 enzyme and thereby diminish the incidence of breast cancer.
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Ferysiuk K, Wójciak KM, Kęska P. Effect of willow herb ( Epilobium angustifolium L.) extract addition to canned meat with reduced amount of nitrite on the antioxidant and other activities of peptides. Food Funct 2022; 13:3526-3539. [PMID: 35253026 DOI: 10.1039/d1fo01534f] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The present study aimed to evaluate the effect of the addition of various amounts (50, 100, 150 and 1000 mg kg-1) of E. angustifolium L. extracts on the biological activity of peptides in canned meat with reduced amount of sodium nitrite and their stability during 180 days of storage (4 °C). The initial peptide data were collected by LC/MS. Antioxidant activities of peptide extracts were detected on the basis of ABTS˙*, FRAP, and iron(II) chelating activity in in vitro tests. A computational study (based on the BIOPEP-UWM database and INNOVAGEN, PeptideRanker and PROTPARAM tools) was also performed to assist in the interpretation of results. The addition of E. angustifolium L. extracts has a positive effect on the peptide profile and various biological activities, the results of which depend on the amount of the extract added to the meat product. However, it should be remembered that the differences between in silico and in vitro experimental environments necessitate further research to confirm the antioxidant behavior of canned meat products supplemented with E. angustifolium L. extract under physiological conditions. Other interactions between the peptide and the food matrix should also be considered as these can lead to chemical and structural modifications that can affect the bioavailability of the bioactive peptides.
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Affiliation(s)
- Karolina Ferysiuk
- Department of Animal Food Technology, Faculty of Food Science and Biotechnology, University of Life Sciences in Lublin, Skromna 8 Street, 20-704 Lublin, Poland.
| | - Karolina Maria Wójciak
- Department of Animal Food Technology, Faculty of Food Science and Biotechnology, University of Life Sciences in Lublin, Skromna 8 Street, 20-704 Lublin, Poland.
| | - Paulina Kęska
- Department of Animal Food Technology, Faculty of Food Science and Biotechnology, University of Life Sciences in Lublin, Skromna 8 Street, 20-704 Lublin, Poland.
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Shaslinah N, Sangavi P, Sangeetha R, Gowthamkumar S, Sindhu V, Langeswaran K. Screening and identification of potential inhibitor for visceral leishmaniasis (VL) through computational analysis. J Genet Eng Biotechnol 2022; 20:35. [PMID: 35195803 PMCID: PMC8866605 DOI: 10.1186/s43141-022-00318-3] [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: 06/20/2021] [Accepted: 02/14/2022] [Indexed: 11/24/2022]
Abstract
Aim The aim of this investigation is to detect potential inhibitor for visceral leishmaniasis through computational analysis. Background Leishmaniasis is categorized as a vector born pathogenic infection prevalent in tropical, subtropical, and in Mediterranean zones spread by intra-macrophage protozoa. The clinical syndrome of leishmaniasis is divided into the following type’s namely cutaneous leishmaniasis, mucocutaneous leishmaniasis, visceral leishmaniasis, and dermal leishmaniasis. Trypanothione synthetase is a key enzyme involving in glutathione biosynthesis as well as hydrolysis. Trypanothione is one of the promising drug targets for parasites. Parasites are inimitable with concern to their dependence on trypanothione to regulate intracellular thiol-redox balance in fighting against oxidative stress and biochemical anxiety. However, trypanothione synthetase was presumed as the target therapeutic alternate in VL therapy. Objective The important objective of this current investigation is to identify or analyze the potential inhibitor for V. leishmaniasis through computational approaches which include virtual screening, molecular docking, ADME prediction, and molecular dynamic simulation. Methods An investigation was performed to develop a 3D protein structure, using computational screening among associated similar structured proteins from popular compound database banks such as Specs, Maybridge, and Enamine, to detect novel staging with a series of validation for emerging innovative drugs molecules. Modeled protein ligand complex was further analyzed to know the binding ability of the complex. Molecular dynamics were performed to ascertain its stability at 50 ns. Results Trypanothione synthetase overall ability in the outcome of series of analysis. Among three database compounds screened, the compound from the Specs database exhibited the better protein-ligand docking scores and fulfilled the drug-like properties through ADMET analysis, and the docked complexes had better stability throughout the simulation. Besides, the other two database leads fulfilled the pharmacological properties, and the complexes were stable in the simulation. Conclusion By analyzing the various compounds from different databases, we concluded that the Specs database compound exhibits potential activity against the target protein and is considered a promising inhibitor for trypanothione synthetase.
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Affiliation(s)
- N Shaslinah
- Cancer Informatics Laboratory, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - P Sangavi
- Cancer Informatics Laboratory, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - R Sangeetha
- Department of Physics, Mannar Thirumalai Naicker College, Pasumalai, Madurai, Tamil Nadu, India
| | - S Gowthamkumar
- Faculty of Allied Health Sciences, Chettinad Hospital & Research Institute, Chettiand Academy of Research and Education, Kelambakkam, Tamil Nadu, India
| | - V Sindhu
- Faculty of Allied Health Sciences, Chettinad Hospital & Research Institute, Chettiand Academy of Research and Education, Kelambakkam, Tamil Nadu, India
| | - K Langeswaran
- Cancer Informatics Laboratory, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India.
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Śliwka-Kaszyńska M, Anusiewicz I, Skurski P. The Mechanism of a Retro-Diels-Alder Fragmentation of Luteolin: Theoretical Studies Supported by Electrospray Ionization Tandem Mass Spectrometry Results. Molecules 2022; 27:1032. [PMID: 35164300 PMCID: PMC8840092 DOI: 10.3390/molecules27031032] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/27/2022] [Accepted: 02/01/2022] [Indexed: 02/06/2023] Open
Abstract
The mechanisms of retro-Diels-Alder fragmentation of luteolin are studied theoretically using the Density Functional Theory method (B3LYP hybrid functional) together with the 6-311++G(d,p) basis set and supported by electrospray ionization tandem mass spectrometry (ESI-MS) results. The reaction paths leading to the formation of 1,3A- and 1,3B- fragment ions observed as the main spectral features in the ESI-MS spectrum are described and discussed, including the structures of the transition states and intermediate products. The heights of the activation energy barriers which have to be overcome along the reaction paths corresponding to 1,3-retrocyclization cleavage of the ionized luteolin are predicted to span the 69-94 kcal/mol range (depending on the initial isomeric structure) for the concerted retrocyclization mechanism and the 60-89 kcal/mol (first barrier) and 24-52 kcal/mol (second barrier) barriers for the stepwise mechanism (also depending on the initial isomeric structure). It is also demonstrated that the final fragmentation products (1,3A- and 1,3B-) are in fact represented by various isomeric systems which are not experimentally distinguishable. In addition, the absence of the spectral feature corresponding to the [M-B]- fragment ion formed by the rupture of the C-C bond connecting luteolin's B and C rings (which does not occur during the ESI-MS experiment) is explained by much larger energy barriers predicted for such a process.
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Affiliation(s)
- Magdalena Śliwka-Kaszyńska
- Department of Organic Chemistry, Faculty of Chemistry, Gdańsk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland;
| | - Iwona Anusiewicz
- Laboratory of Quantum Chemistry, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland;
| | - Piotr Skurski
- Laboratory of Quantum Chemistry, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland;
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Kęska P, Stadnik J. Potential DPP IV Inhibitory Peptides from Dry-Cured Pork Loins after Hydrolysis: An In Vitro and In Silico Study. Curr Issues Mol Biol 2021; 43:1335-1349. [PMID: 34698081 PMCID: PMC8928953 DOI: 10.3390/cimb43030095] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/22/2021] [Accepted: 09/23/2021] [Indexed: 12/28/2022] Open
Abstract
Peptidyl peptidase IV (DPP-IV) is a pharmacotherapeutic target in type 2 diabetes, and inhibitors of this enzyme are an important class of drugs for the treatment of type 2 diabetes. In the present study, peptides (<7 kDa) isolated from dry-cured pork loins after pepsin and pancreatin hydrolysis were identified by mass spectrometry and tested as potential inhibitors of DPP-IV by the in silico method. Two peptides, namely WTIAVPGPPHS from myomesin (water-soluble fraction, A = 0.9091) and FKRPPL from troponin (salt-soluble fraction, A = 0.8333), were selected as the most promising inhibitors of DPP-IV. Both peptides were subjected to ADMET analysis. Fragments of these peptides showed promising drug-likeness properties as well as favorable absorption, distribution, metabolism, excretion, and toxicity functions, suggesting that they are novel leads in the development of DPP-IV inhibitors from food.
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12
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Benjakul S, Singh A, Chotphruethipong L, Mittal A. Protein-polyphenol conjugates: Preparation, functional properties, bioactivities and applications in foods and nutraceuticals. ADVANCES IN FOOD AND NUTRITION RESEARCH 2021; 98:281-320. [PMID: 34507645 DOI: 10.1016/bs.afnr.2021.02.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Protein is a crucial nutritional ingredient in the daily human diet. Polyphenols (PPNs) are the abundant phytochemicals in plants, which are associated with health promotion as well as affect functionality in food systems. Both ingredients possess different types of functionalities (crosslinking, gelling, emulsifying, film-forming, etc.) and bioactivities (antioxidant, antimicrobial, anti-inflammatory, etc.). In the past decade, various methods have been implemented to enhance the functionalities and bioactivities of foods. Conjugation or grafting methods has been introduced widely. Conjugations of PPNs with proteins through various methods have been performed for the synthesis of the protein-polyphenol conjugate. Those potential grafting methods are alkaline associated, free-radical mediated, enzyme catalyzed, and chemical coupling methods. Several factors such as reaction conditions, type of proteins, and PPNs also influenced the conjugation efficiency. Various technologies, e.g., mass spectroscopy, fluorescence spectroscopy, UV spectroscopy, Fourier transform infrared spectroscopy, circular dichroism, and sodium dodecyl sulfate polyacrylamide gel electrophoresis have been used to elucidate conjugation and structural alternation of proteins and some properties of resulting conjugates. The prepared protein-PPN conjugates have been documented to enhance the bioactivities and functional properties of an initial protein. Moreover, conjugates have been employed in emulsions or as nanoparticles for nutraceutical delivery. Edible-films for food packaging and hydrogels for controlled drug release have been developed using protein-PPN conjugates. This chapter focuses on the methodologies and characteristics of protein-PPN conjugates and their applications in various food systems and nutraceutical field.
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Affiliation(s)
- Soottawat Benjakul
- International Center of Excellence in Seafood Science and Innovation, Faculty of Agro-Industry, Prince of Songkla University, Hat Yai, Songkhla, Thailand.
| | - Avtar Singh
- International Center of Excellence in Seafood Science and Innovation, Faculty of Agro-Industry, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Lalita Chotphruethipong
- International Center of Excellence in Seafood Science and Innovation, Faculty of Agro-Industry, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Ajay Mittal
- International Center of Excellence in Seafood Science and Innovation, Faculty of Agro-Industry, Prince of Songkla University, Hat Yai, Songkhla, Thailand
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Renganathan S, Manokaran S, Vasanthakumar P, Singaravelu U, Kim PS, Kutzner A, Heese K. Phytochemical Profiling in Conjunction with In Vitro and In Silico Studies to Identify Human α-Amylase Inhibitors in Leucaena leucocephala (Lam.) De Wit for the Treatment of Diabetes Mellitus. ACS OMEGA 2021; 6:19045-19057. [PMID: 34337243 PMCID: PMC8320072 DOI: 10.1021/acsomega.1c02350] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 07/05/2021] [Indexed: 05/12/2023]
Abstract
Bioactive constituents from natural sources are of great interest as alternatives to synthetic compounds for the treatment of various diseases, including diabetes mellitus. In the present study, phytochemicals present in Leucaena leucocephala (Lam.) De Wit leaves were identified by gas chromatography-mass spectrometry and further examined by qualitative and quantitative methods. α-Amylase enzyme activity assays were performed and revealed that L. leucocephala (Lam.) De Wit leaf extract inhibited enzyme activity in a dose-dependent manner, with efficacy similar to that of the standard α-amylase inhibitor acarbose. To determine which phytochemicals were involved in α-amylase enzyme inhibition, in silico virtual screening of the absorption, distribution, metabolism, excretion, and toxicity properties was performed and pharmacophore dynamics were assessed. We identified hexadecenoic acid and oleic acid ((Z)-octadec-9-enoic acid) as α-amylase inhibitors. The binding stability of α-amylase to those two fatty acids was confirmed in silico by molecular docking and a molecular dynamics simulation performed for 100 ns. Together, our findings indicate that L. leucocephala (Lam.) De Wit-derived hexadecanoic acid and oleic acid are natural product-based antidiabetic compounds that can potentially be used to manage diabetes mellitus.
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Affiliation(s)
- Senthil Renganathan
- Department
of Bioinformatics, Marudupandiyar College, Thanjavur 613403, Tamil Nadu, India
| | - Sakthivel Manokaran
- Department
of Bioinformatics, Bharathiar University, Coimbatore 641046, Tamil Nadu, India
| | - Preethi Vasanthakumar
- Department
of Biotechnology, Bharath College of Science
and Management, Thanjavur 613005, Tamil Nadu, India
| | - Usha Singaravelu
- Department
of Bioinformatics, Bharathiar University, Coimbatore 641046, Tamil Nadu, India
| | - Pok-Son Kim
- Department
of Mathematics, Kookmin University, 77 Jeongneung-ro, Seongbuk-gu, Seoul 136-702, Republic of Korea
| | - Arne Kutzner
- Department
of Information Systems, College of Computer Science, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul 133-791, Republic of Korea
| | - Klaus Heese
- Graduate
School of Biomedical Science and Engineering, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul 133-791, Republic of Korea
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14
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Lamazares E, MacLeod-Carey D, Miranda FP, Mena-Ulecia K. Theoretical Evaluation of Novel Thermolysin Inhibitors from Bacillus thermoproteolyticus. Possible Antibacterial Agents. Molecules 2021; 26:E386. [PMID: 33451037 PMCID: PMC7828527 DOI: 10.3390/molecules26020386] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/10/2021] [Accepted: 01/11/2021] [Indexed: 01/29/2023] Open
Abstract
The search for new antibacterial agents that could decrease bacterial resistance is a subject in continuous development. Gram-negative and Gram-positive bacteria possess a group of metalloproteins belonging to the MEROPS peptidase (M4) family, which is the main virulence factor of these bacteria. In this work, we used the previous results of a computational biochemistry protocol of a series of ligands designed in silico using thermolysin as a model for the search of antihypertensive agents. Here, thermolysin from Bacillus thermoproteolyticus, a metalloprotein of the M4 family, was used to determine the most promising candidate as an antibacterial agent. Our results from docking, molecular dynamics simulation, molecular mechanics Poisson-Boltzmann (MM-PBSA) method, ligand efficiency, and ADME-Tox properties (Absorption, Distribution, Metabolism, Excretion, and Toxicity) indicate that the designed ligands were adequately oriented in the thermolysin active site. The Lig783, Lig2177, and Lig3444 compounds showed the best dynamic behavior; however, from the ADME-Tox calculated properties, Lig783 was selected as the unique antibacterial agent candidate amongst the designed ligands.
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Affiliation(s)
- Emilio Lamazares
- Pathophysiology Department, Biotechnology and Biopharmaceutical Laboratory, School of Biological Sciences, Universidad de Concepción, Victor Lamas 1290, P.O. Box 160-C, Concepción 4079386, Chile;
| | - Desmond MacLeod-Carey
- Inorganic Chemistry and Molecular Materials Center, Instituto de Ciencias Químicas Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, El Llano Subercaseaux 2801, San Miguel, Santiago 8900000, Chile;
| | - Fernando P. Miranda
- Instituto de Fisiología, Facultad de Medicina, Universidad Austral de Chile, Valdivia 5090000, Chile;
| | - Karel Mena-Ulecia
- Departamento de Ciencias Biológicas y Químicas, Facultad de Recursos Naturales, Universidad Católica de Temuco, Ave. Rudecindo Ortega 02950, Temuco 4780000, Chile
- Núcleo de Investigación en Bioproductos y Materiales Avanzados (BIOMA), Facultad de Ingeniería, Universidad Católica de Temuco, Ave. Rudecindo Ortega 02950, Temuco 4780000, Chile
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15
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Fan Y, Yu Z, Zhao W, Ding L, Zheng F, Li J, Liu J. Identification and molecular mechanism of angiotensin-converting enzyme inhibitory peptides from Larimichthys crocea titin. FOOD SCIENCE AND HUMAN WELLNESS 2020. [DOI: 10.1016/j.fshw.2020.04.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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16
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Kumar N, Gorai B, Gupta S, Shiva, Goel N. Extrapolation of hydroxytyrosol and its analogues as potential anti-inflammatory agents. J Biomol Struct Dyn 2020; 39:5588-5599. [PMID: 32672527 DOI: 10.1080/07391102.2020.1792990] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Discovery of potential lead molecule is a challenging, and complex process which require lots of money, patience, and manpower. Human beings are using natural products, predominantly secondary metabolites, for this purpose since ancient time and they are still working on them as a potent source for drug discovery due to their wide structural diversity. Phenolic phytochemicals such as hydroxytyrosol and tyrosol are natural antioxidant and involved in many biological disease cure. Herein, we have carried out the quantum chemical calculations for conformational analysis, geometry optimization and computation of electronic as well as optical properties of hydroxytyrosol and its analogues (1a-1k) in terms of density functional theory by using Gaussian 09 program suite. The eventual charge transfer within the molecules has been confirmed by the analysis of frontier molecular orbitals. The molecular docking studies of 1a-1k with cyclooxygenase-2 showed the noticeable binding affinity as compared to other nonsteroidal anti-inflammatory drugs viz. aspirin, naproxen and celecoxib. Computation of pharmacokinetics and pharmacological properties confirmed the lead/drug like potential of these screened molecules. Furthermore, the molecular dynamics simulation of best three docked ligands (1f, 1h and 1k)-receptor complex and their binding free energy calculations reveals that these molecules bind in the catalytic cavity of cyclooxygenase-2 and found stable during the 100 ns of simulation. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Naresh Kumar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Madhya Pradesh, India
| | - Biswajit Gorai
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore, India
| | - Saurabh Gupta
- AgriGenome labs Pvt. Ltd. SINC, IKP Knowledge Park, Genome Valley, Hyderabad, India
| | - Shiva
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Nidhi Goel
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, India
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17
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Oxygenated xanthones as P-glycoprotein modulators at the intestinal barrier: in vitro and docking studies. Med Chem Res 2020. [DOI: 10.1007/s00044-020-02544-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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18
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Biological evaluation and interaction mechanism of beta-site APP cleaving enzyme 1 inhibitory pentapeptide from egg albumin. FOOD SCIENCE AND HUMAN WELLNESS 2020. [DOI: 10.1016/j.fshw.2020.01.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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19
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MacLeod-Carey D, Solis-Céspedes E, Lamazares E, Mena-Ulecia K. Evaluation of new antihypertensive drugs designed in silico using Thermolysin as a target. Saudi Pharm J 2020; 28:582-592. [PMID: 32435139 PMCID: PMC7229335 DOI: 10.1016/j.jsps.2020.03.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 03/18/2020] [Indexed: 12/18/2022] Open
Abstract
The search for new therapies for the treatment of Arterial hypertension is a major concern in the scientific community. Here, we employ a computational biochemistry protocol to evaluate the performance of six compounds (Lig783, Lig1022, Lig1392, Lig2177, Lig3444 and Lig6199) to act as antihypertensive agents. This protocol consists of Docking experiments, efficiency calculations of ligands, molecular dynamics simulations, free energy, pharmacological and toxicological properties predictions (ADME-Tox) of the six ligands against Thermolysin. Our results show that the docked structures had an adequate orientation in the pocket of the Thermolysin enzymes, reproducing the X-ray crystal structure of Inhibitor-Thermolysin complexes in an acceptable way. The most promising candidates to act as antihypertensive agents among the series are Lig2177 and Lig3444. These compounds form the most stable ligand-Thermolysin complexes according to their binding free energy values obtained in the docking experiments as well as MM-GBSA decomposition analysis calculations. They present the lowest values of Ki, indicating that these ligands bind strongly to Thermolysin. Lig2177 was oriented in the pocket of Thermolysin in such a way that both OH of the dihydroxyl-amino groups to establish hydrogen bond interactions with Glu146 and Glu166. In the same way, Lig3444 interacts with Asp150, Glu143 and Tyr157. Additionally, Lig2177 and Lig3444 fulfill all the requirements established by Lipinski Veber and Pfizer 3/75 rules, indicating that these compounds could be safe compounds to be used as antihypertensive agents. We are confident that our computational biochemistry protocol can be used to evaluate and predict the behavior of a broad range of compounds designed in silicoagainst a protein target.
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Affiliation(s)
- Desmond MacLeod-Carey
- Universidad Autónoma de Chile, Facultad de Ingeniería, Instituto de Ciencias Químicas Aplicadas, Inorganic Chemistry and Molecular Materials Center, El Llano Subercaseaux 2801, San Miguel, Santiago, Chile
| | - Eduardo Solis-Céspedes
- Vicerrectoría de Investigación y Postgrado, Universidad Católica del Maule, 3460000 Talca, Chile
| | - Emilio Lamazares
- Universidad de Concepción, Biotechnology and Biopharmaceutical Laboratory, Pathophysiology Department, School of Biological Sciences, Victor Lamas 1290, P.O. Box 160-C, Concepción, Chile
| | - Karel Mena-Ulecia
- Universidad Católica de Temuco, Facultad de Recursos Naturales, Departamento de Ciencias Biolígicas y Químicas, Ave. Rudecindo Ortega #02950, Temuco, Chile
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20
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Kumar N, Goel N. Phenolic acids: Natural versatile molecules with promising therapeutic applications. ACTA ACUST UNITED AC 2019; 24:e00370. [PMID: 31516850 PMCID: PMC6734135 DOI: 10.1016/j.btre.2019.e00370] [Citation(s) in RCA: 524] [Impact Index Per Article: 104.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 07/04/2019] [Accepted: 08/12/2019] [Indexed: 01/19/2023]
Abstract
Plant phenolics are considered to be a vital human dietary component and exhibit a tremendous antioxidant activity as well as other health benefits. Epidemiology evidence indicates that a diet rich in antioxidant fruits and vegetables significantly reduces the risk of many oxidative stress related diseases viz. cancers, diabetes and cardiovascular. The number and position of hydroxyl group in a particular phenolic compound leads to the variation in their antioxidant potential. Polyphenols are the main source of dietary antioxidants, and are effortlessly absorbed in the intestine. Phenolic acids, a sub class of plant phenolics, possess phenol moiety and resonance stabilized structure which causes the H-atom donation results in antioxidant property through radical scavenging mechanism. Other mode such as radical quenching via electron donation and singlet oxygen quenching are also known for the antioxidant activity of phenolic acids. Furthermore, phenolic acids are found ubiquitously and well documented for other health protective effects like antimicrobial, anticancer, anti-inflammatory, anti-mutagenic etc. The contribution emphasize on the phenolic acids potential in drug discovery. In addition their occurrence, biosynthesis, metabolism and health effects are discussed in detail.
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Affiliation(s)
- Naresh Kumar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol Campus, Indore, Madhya Pradesh-453552, India
| | - Nidhi Goel
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh-221005, India
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21
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Yadav TC, Kumar N, Raj U, Goel N, Vardawaj PK, Prasad R, Pruthi V. Exploration of interaction mechanism of tyrosol as a potent anti-inflammatory agent. J Biomol Struct Dyn 2019; 38:382-397. [PMID: 30887884 DOI: 10.1080/07391102.2019.1575283] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Drug discovery for a vigorous and feasible lead candidate is a challenging scientific mission as it requires expertise, experience, and huge investment. Natural products and their derivatives having structural diversity are renowned source of therapeutic agents since many years. Tyrosol (a natural phenylethanoid) has been extracted from olive oil, and its structure was confirmed by elemental analysis, FT-IR, FT-NMR, and single crystal X-ray crystallography. The conformational analysis for tyrosol geometry was performed by Gaussian 09 in terms of density functional theory. Validation of bond lengths and bond angles obtained experimentally as well as theoretically were performed with the help of curve fitting analysis, and values of correlation coefficient (R) obtained as 0.988 and 0.984, respectively. The charge transfer within the tyrosol molecule was confirmed by analysis of HOMO→LUMO molecular orbitals. In molecular docking with COX-2 (PDB ID: 5F1A), tyrosol was found to possess satisfactory binding affinity as compared to other NSAIDs (Aspirin, Ibuprofen, and Naproxen) and a COX-2 selective drug (Celecoxib). ADMET prediction, drug-likeness and bioactivity score altogether confirm the lead/drug like potential of tyrosol. Further investigation of simulation quality plot, RMSD and RMSF plots, ligands behavior plot as well as post simulation analysis manifest the consistency of 5F1A-tyrosol complex throughout the 20 ns molecular simulation process that signifies its compactness and stability within the receptor pocket. AbbreviationsADMETAbsorption, Distribution, Metabolism, Excretion and ToxicityÅAngstromCOX-2Cyclooxygenase-2DFTDensity Functional TheoryDMFDimethylformamideFMOFrontier Molecular OrbitalFT-IRFourier-transform Infrared SpectroscopyFT-NMRNuclear Magnetic Resonance SpectroscopyHOMOHighest Occupied Molecular OrbitalLUMOLowest Unoccupied Molecular OrbitalMDMolecular DynamicsNSNanosecondNSAIDsNon-steroidal anti-inflammatory drugsOPEOsiris Property ExplorerRMSDRoot-Mean-Square DeviationRMSFRoot Sean Square FluctuationCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Tara Chand Yadav
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Naresh Kumar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Utkarsh Raj
- Department of Bioinformatics, Indian Institute of Information Technology Allahabad, Allahabad, India
| | - Nidhi Goel
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Pritish Kumar Vardawaj
- Department of Bioinformatics, Indian Institute of Information Technology Allahabad, Allahabad, India
| | - Ramasare Prasad
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Vikas Pruthi
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
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22
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Kumar N, Gupta S, Chand Yadav T, Pruthi V, Kumar Varadwaj P, Goel N. Extrapolation of phenolic compounds as multi-target agents against cancer and inflammation. J Biomol Struct Dyn 2018; 37:2355-2369. [PMID: 30047324 DOI: 10.1080/07391102.2018.1481457] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Natural products acquire massive structural and chemical diversity, which cannot be coordinated by any synthetic libraries for small molecules and they are continuing to inspire novel discoveries in health sciences. We have performed the computational calculations for geometry optimization and prediction of electronic and structural properties of some plant phenolic compounds through Gaussian 09 program. Energies of molecular orbitals were computed, to mimic out the stabilities arising from charge delocalization and intramolecular interactions. This process indicated the eventual charge transfer within the molecules. The molecular docking and ADMET properties of these compounds with a novel anticancer (HER2) and anti-inflammatory (COX-2) targets revealed that two molecules were capable of inhibiting both the targets, and could be used as multi target inhibitors. Furthermore, molecular dynamics simulation studies were performed to elucidate the binding mechanism and the comparison of inhibitor's binding mode with diverse biological activities as anticancer and anti-inflammatory agents. A high-quality association was reported among quantum chemical, ADMET, docking, dynamics and MMGBSA results. Communicated By Ramaswamy H. Sarma.
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Affiliation(s)
- Naresh Kumar
- a Department of Biotechnology , Indian Institute of Technology Roorkee , Roorkee 247667 , Uttarakhand , India;,b Discipline of Biosciences and Biomedical Engineering , Indian Institute of Technology Indore , Indore 453552, Madhya Pradesh , India
| | - Saurabh Gupta
- c Department of Bioinformatics , Indian Institute of Information Technology , Allahabad 211015 , India
| | - Tara Chand Yadav
- a Department of Biotechnology , Indian Institute of Technology Roorkee , Roorkee 247667 , Uttarakhand , India
| | - Vikas Pruthi
- a Department of Biotechnology , Indian Institute of Technology Roorkee , Roorkee 247667 , Uttarakhand , India
| | - Pritish Kumar Varadwaj
- c Department of Bioinformatics , Indian Institute of Information Technology , Allahabad 211015 , India
| | - Nidhi Goel
- d Department of Chemistry, Institute of Science , Banaras Hindu University , Varanasi 221005 , India
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23
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Yu Z, Fan Y, Zhao W, Ding L, Li J, Liu J. Novel Angiotensin-Converting Enzyme Inhibitory Peptides Derived from Oncorhynchus mykiss Nebulin: Virtual Screening and In Silico Molecular Docking Study. J Food Sci 2018; 83:2375-2383. [PMID: 30101981 DOI: 10.1111/1750-3841.14299] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Revised: 06/08/2018] [Accepted: 06/24/2018] [Indexed: 12/17/2022]
Abstract
Excessive concentrations of angiotensin-converting enzyme (ACE) can give rise to high blood pressure, and is harmful to the body. ACE inhibitory peptides from food proteins are considered good sources of function food. However, the preparation of ACE inhibitory peptides by classical method faces many challenges. Three novel ACE inhibitory peptides were identified by in silico methods, and showed potent activity against ACE in vitro. The simulation hydrolysis of nebulin was performed with ExPASy PeptideCutter program. Potential activity, solubility, and absorption, distribution, metabolism, excretion, and toxicity properties of generated peptides were predicted using program online. Molecular docking displayed that EGF, HGR, and VDF were docked into the S1 and S2 pockets of ACE. Meanwhile, Phe and Arg at the C-terminal enhance ACE affinity. The IC50 values of EGF, HGR, and VDF were 474.65 ± 0.08, 106.21 ± 0.52, and 439.27 ± 0.09 μM, respectively. Three peptides EGF, HGR, and VDF from Oncorhynchus mykiss nebulin were identified, and the molecular mechanism between ACE and peptides was clarified using in silico methods. The results suggested that Oncorhynchus mykiss nebulin would be an attractive raw material of antihypertensive nutraceutical ingredients. PRACTICAL APPLICATION This study has shown the potential of Oncorhynchus mykiss nebulin as good sources for producing ACE inhibitory peptides. According to this finding, in silico approach is the feasible way for prediction and identification of food-derived ACE inhibitory peptides in emerging nutraceutical field.
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Affiliation(s)
- Zhipeng Yu
- College of Food Science and Engineering, Bohai Univ., Jinzhou, 121013, P.R. China
| | - Yue Fan
- College of Food Science and Engineering, Bohai Univ., Jinzhou, 121013, P.R. China
| | - Wenzhu Zhao
- College of Food Science and Engineering, Bohai Univ., Jinzhou, 121013, P.R. China
| | - Long Ding
- Lab of Nutrition and Functional Food, Jilin Univ., Changchun, 130062, P.R. China
| | - Jianrong Li
- College of Food Science and Engineering, Bohai Univ., Jinzhou, 121013, P.R. China
| | - Jingbo Liu
- Lab of Nutrition and Functional Food, Jilin Univ., Changchun, 130062, P.R. China
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24
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Razzaghi-Asl N, Mirzayi S, Mahnam K, Sepehri S. Identification of COX-2 inhibitors via structure-based virtual screening and molecular dynamics simulation. J Mol Graph Model 2018; 83:138-152. [DOI: 10.1016/j.jmgm.2018.05.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 05/20/2018] [Accepted: 05/23/2018] [Indexed: 01/31/2023]
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