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Rani N, Kumar P. Exploring Natural Compounds as Potential CDK4 Inhibitors for Therapeutic Intervention in Neurodegenerative Diseases through Computational Analysis. Mol Biotechnol 2024:10.1007/s12033-024-01258-8. [PMID: 39207668 DOI: 10.1007/s12033-024-01258-8] [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: 03/27/2024] [Accepted: 07/03/2024] [Indexed: 09/04/2024]
Abstract
CDK4 is a member of the serine-threonine kinase family, which has been found to be overexpressed in a plethora of studies related to neurodegenerative diseases. CDK4 is one of the most validated therapeutic targets for neurodegenerative diseases. Hence, the discovery of potent inhibitors of CDK4 is a promising candidate in the drug discovery field. Firstly, the reference drug Palbociclib was identified from the available literature as a potential candidate against target CDK4. In the present study, the Collection of Open Natural Products (COCONUT) database was accessed for determining potential CDK4 inhibitors using computational approaches based on the Tanimoto algorithm for similarity with the target drug, i.e., Palbociclib. The potential candidates were analyzed using SWISSADME, and the best candidates were filtered based on Lipinski's Rule of 5, Brenk, blood-brain barrier permeability, and Pains parameter. Further, the molecular docking protocol was accessed for the filtered compounds to anticipate the CDK4-ligand binding score, which was validated by the fastDRH web-based server. Based on the best docking score so obtained, the best four natural compounds were chosen for further molecular dynamic simulation to assess their stability with CDK4. In this study, two natural products, with COCONUT Database compound ID-CNP0396493 and CNP0070947, have been identified as the most suitable candidates for neuroprotection.
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Affiliation(s)
- Neetu Rani
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly DCE), Shahbad Daulatpur, Bawana Road, Delhi, 110042, India
| | - Pravir Kumar
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly DCE), Shahbad Daulatpur, Bawana Road, Delhi, 110042, India.
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University, Delhi, 110042, India.
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2
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Ariga K. 2D Materials Nanoarchitectonics for 3D Structures/Functions. MATERIALS (BASEL, SWITZERLAND) 2024; 17:936. [PMID: 38399187 PMCID: PMC10890396 DOI: 10.3390/ma17040936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 02/09/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024]
Abstract
It has become clear that superior material functions are derived from precisely controlled nanostructures. This has been greatly accelerated by the development of nanotechnology. The next step is to assemble materials with knowledge of their nano-level structures. This task is assigned to the post-nanotechnology concept of nanoarchitectonics. However, nanoarchitectonics, which creates intricate three-dimensional functional structures, is not always easy. Two-dimensional nanoarchitectonics based on reactions and arrangements at the surface may be an easier target to tackle. A better methodology would be to define a two-dimensional structure and then develop it into a three-dimensional structure and function. According to these backgrounds, this review paper is organized as follows. The introduction is followed by a summary of the three issues; (i) 2D to 3D dynamic structure control: liquid crystal commanded by the surface, (ii) 2D to 3D rational construction: a metal-organic framework (MOF) and a covalent organic framework (COF); (iii) 2D to 3D functional amplification: cells regulated by the surface. In addition, this review summarizes the important aspects of the ultimate three-dimensional nanoarchitectonics as a perspective. The goal of this paper is to establish an integrated concept of functional material creation by reconsidering various reported cases from the viewpoint of nanoarchitectonics, where nanoarchitectonics can be regarded as a method for everything in materials science.
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Affiliation(s)
- Katsuhiko Ariga
- Research Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba 305-0044, Ibaraki, Japan;
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa 277-8561, Chiba, Japan
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3
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Ariga K. Materials Nanoarchitectonics at Dynamic Interfaces: Structure Formation and Functional Manipulation. MATERIALS (BASEL, SWITZERLAND) 2024; 17:271. [PMID: 38204123 PMCID: PMC10780059 DOI: 10.3390/ma17010271] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 12/25/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024]
Abstract
The next step in nanotechnology is to establish a methodology to assemble new functional materials based on the knowledge of nanotechnology. This task is undertaken by nanoarchitectonics. In nanoarchitectonics, we architect functional material systems from nanounits such as atoms, molecules, and nanomaterials. In terms of the hierarchy of the structure and the harmonization of the function, the material created by nanoarchitectonics has similar characteristics to the organization of the functional structure in biosystems. Looking at actual biofunctional systems, dynamic properties and interfacial environments are key. In other words, nanoarchitectonics at dynamic interfaces is important for the production of bio-like highly functional materials systems. In this review paper, nanoarchitectonics at dynamic interfaces will be discussed, looking at recent typical examples. In particular, the basic topics of "molecular manipulation, arrangement, and assembly" and "material production" will be discussed in the first two sections. Then, in the following section, "fullerene assembly: from zero-dimensional unit to advanced materials", we will discuss how various functional structures can be created from the very basic nanounit, the fullerene. The above examples demonstrate the versatile possibilities of architectonics at dynamic interfaces. In the last section, these tendencies will be summarized, and future directions will be discussed.
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Affiliation(s)
- Katsuhiko Ariga
- Research Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba 305-0044, Ibaraki, Japan;
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa 277-8561, Chiba, Japan
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4
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Singh AK, Pal P, Pandey B, Goksen G, Sahoo UK, Lorenzo JM, Sarangi PK. Development of "Smart Foods" for health by nanoencapsulation: Novel technologies and challenges. Food Chem X 2023; 20:100910. [PMID: 38144773 PMCID: PMC10740092 DOI: 10.1016/j.fochx.2023.100910] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 09/18/2023] [Accepted: 09/27/2023] [Indexed: 12/26/2023] Open
Abstract
Importance of nanotechnology may be seen by penetration of its application in diverse areas including the food sector. With investigations and advancements in nanotechnology, based on feedback from these diverse areas, ease, and efficacy are also increasing. The food sector may use nanotechnology to encapsulate smart foods for increased health, wellness, illness prevention, and effective targeted delivery. Such nanoencapsulated targeted delivery systems may further add to the economic and nutritional properties of smart foods like stability, solubility, effectiveness, safeguard against disintegration, permeability, and bioavailability of smart/bioactive substances. But in the way of application, the fabrication of nanomaterials/nanostructures has several challenges which range from figuring out the optimal technique for obtaining them to determining the most suitable form of nanostructure for a bioactive molecule of interest. This review precisely addresses concepts, recent advances in fabrication techniques as well as current challenges/glitches of nanoencapsulation with special reference to smart foods/bioactive components. Since dealing with food materials also raises the quest for safety and regulatory norms a brief overview of the safety and regulatory aspects of nanomaterials/nanoencapsulation is also presented.
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Affiliation(s)
- Akhilesh Kumar Singh
- Department of Biotechnology, School of Life Sciences, Mahatma Gandhi Central University, Motihari, Bihar 845401, India
| | - Priti Pal
- Shri Ramswaroop Memorial College of Engineering & Management, Tewariganj, Faizabad, Road, Lucknow 226028, India
| | - Brijesh Pandey
- Department of Biotechnology, School of Life Sciences, Mahatma Gandhi Central University, Motihari, Bihar 845401, India
| | - Gulden Goksen
- Department of Food Technology, Vocational School of Technical Sciences at Mersin Tarsus Organized Industrial Zone, Tarsus University, Mersin 33100, Turkey
| | | | - Jose M. Lorenzo
- Centro Tecnológico de la Carne de Galicia, Avda. Galicia n◦ 4, Parque Tecnológico de Galicia, San Cibrao das Viñas, 32900 Ourense, Spain
| | - Prakash Kumar Sarangi
- College of Agriculture, Central Agricultural University, Imphal 795004, Manipur, India
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Khalid A, Ali S, Rukhma, Jahangeer M, Sarwar A, Nelofer R, Aziz T, Alharbi M, Alasmari AF, Albekairi TH. Immobilization of Aspergillus oryzae tyrosine hydroxylase on ZnO nanocrystals for improved stability and catalytic efficiency towards L-dopa production. Sci Rep 2023; 13:22882. [PMID: 38129644 PMCID: PMC10739923 DOI: 10.1038/s41598-023-50198-x] [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: 10/10/2023] [Accepted: 12/16/2023] [Indexed: 12/23/2023] Open
Abstract
The current study focuses on the submerged fermentation of tyrosine hydroxylase (TH) from Aspergillus oryzae IIB-9 and its immobilization on zinc oxide nanocrystals (ZnO-NPs) for increased L-dopa production. The volume of Vogel's medium (75 ml), period of incubation (72 h), initial pH (5.5), and size of inoculum (1.5 ml) were optimal for maximum TH activity. The watch glass-dried (WG) and filter paper-dried (FP) ZnO-NPs were prepared and characterized using analytical techniques. The UV-Vis spectra revealed 295 and 285 nm absorption peaks for WG-ZnO-NPs and FP-ZnO-NPs dispersed in isopropanol. X-ray diffraction analysis confirmed the crystalline nature of ZnO-NPs. FTIR spectra band from 740 to 648.1/cm and 735.8/cm to 650.1/cm showed the stretching vibrations of WG-ZnO-NPs and FP-ZnO-NPs, respectively. The particle size of ZnO-NPs observed by scanning electron microscopy (SEM) images was between 130 and 170 nm. Furthermore, the stability of immobilized TH on ZnO-NPs was determined by varying the incubation period (10 min for WG-NPs and 15 min for FP-NPs) and temperature (45 °C and 30 °C for WG and FP-NPs, respectively). Incubating enzymes with various copper, iron, manganese, and zinc salts studied the catalytic efficiency of TH. Immobilization of TH on ZnO-NPs resulted in an 11.05-fold increase in TH activity, thus enhancing stability and catalytic efficiency.
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Affiliation(s)
- Ansa Khalid
- Institute of Industrial Biotechnology, Government College University, Lahore, Pakistan
| | - Sikander Ali
- Institute of Industrial Biotechnology, Government College University, Lahore, Pakistan.
| | - Rukhma
- Institute of Industrial Biotechnology, Government College University, Lahore, Pakistan
- Food and Biotechnology Research Center, PCSIR Laboratories Complex Ferozpur Road, Lahore, Pakistan
| | - Muhammad Jahangeer
- Food and Biotechnology Research Center, PCSIR Laboratories Complex Ferozpur Road, Lahore, Pakistan
| | - Abid Sarwar
- Food and Biotechnology Research Center, PCSIR Laboratories Complex Ferozpur Road, Lahore, Pakistan
| | - Rubina Nelofer
- Food and Biotechnology Research Center, PCSIR Laboratories Complex Ferozpur Road, Lahore, Pakistan
| | - Tariq Aziz
- Laboratory of Animal Health, Food Hygiene, and Quality, Department of Agriculture, University of Ioannina, 471 32, Arta, Greece.
| | - Metab Alharbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 2455, 11451, Riyadh, Saudi Arabia
| | - Abdullah F Alasmari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 2455, 11451, Riyadh, Saudi Arabia
| | - Thamer H Albekairi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 2455, 11451, Riyadh, Saudi Arabia
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6
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Shabbir MA, Naveed M, Rehman SU, Ain NU, Aziz T, Alharbi M, Alsahammari A, Alasmari AF. Synthesis of Iron Oxide Nanoparticles from Madhuca indica Plant Extract and Assessment of Their Cytotoxic, Antioxidant, Anti-Inflammatory, and Anti-Diabetic Properties via Different Nanoinformatics Approaches. ACS OMEGA 2023; 8:33358-33366. [PMID: 37744851 PMCID: PMC10515396 DOI: 10.1021/acsomega.3c02744] [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: 04/24/2023] [Accepted: 08/24/2023] [Indexed: 09/26/2023]
Abstract
Recently, nanobiotechnology has attracted a lot of attention, as it is a rapidly emerging field that is still growing and developing efficient and advanced therapeutic protocols under the umbrella of nanomedicine. It can revolutionize solutions to biomedical problems by developing effective treatment protocols and therapeutics. However, focus and research are still required to make these therapeutics more effective and safer to use. In this study, iron oxide nanoparticles were synthesized from Madhuca indica extract using green synthesis protocols. The nanoparticles were further characterized based on their absorption spectrum, size, structural morphology, and other related parameters. Biological assays were also performed to evaluate biological applications for the synthesized nanoparticles. In silico analysis was performed to assess the druglike properties of synthesized nanoparticles. The results proved an optimized synthesis of the iron oxide nanoparticles with the size of 56 nm confirmed by SEM. The FTIR analysis predicted the presence of nitro and carbonyl groups in the synthesized nanoparticles. The 81% DPPH inhibition confirmed the antioxidant activity, and the 96.20% inhibition of egg albumin protein confirmed the anti-inflamatory activity. Additionally, the 73.26% inhibition of α-amylase, which was more than that of the control used, confirmed the antidiabetic activity. The ADMET analysis confirmed the synthesized nanoparticles as potential therapeutic candidates as well. However, further evaluation for safety concerns is still required to use these FeONPs as potential therapeutic agents. This study can be proved as a significant contribution to the scientific community and a gateway to the future scientists who are willing to work on nanomedicine and nanobiotechnology. ADMET analysis confirmed the synthesized nanoparticles as potential therapeutic candidates as well. However, further evaluation for safety concerns is still required to use these FeONPs and potential therapeutic agents.
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Affiliation(s)
- Muhammad Aqib Shabbir
- Department
of Biotechnology, Faculty of Life Science & Technology, University of Central Punjab, Lahore 54590, Pakistan
| | - Muhammad Naveed
- Department
of Biotechnology, Faculty of Life Science & Technology, University of Central Punjab, Lahore 54590, Pakistan
| | - Shafiq ur Rehman
- Department
of Basic and Applied Chemistry, Faculty of Science & Technology, University of Central Punjab, Lahore 54000, Pakistan
| | - Noor ul Ain
- Department
of Biotechnology, Faculty of Life Science & Technology, University of Central Punjab, Lahore 54590, Pakistan
| | - Tariq Aziz
- Department
of Agriculture University of Ioannina, Arta 47100, Greece
| | - Metab Alharbi
- Department
of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Abdulrahman Alsahammari
- Department
of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Abdullah F. Alasmari
- Department
of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
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7
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Shouket S, Khurshid S, Khan J, Batool R, Sarwar A, Aziz T, Alhomrani M, Alamri AS, Sameeh MY, Zubair Filimban F. Enhancement of shelf-life of food items via immobilized enzyme nanoparticles on varied supports. A sustainable approach towards food safety and sustainability. Food Res Int 2023; 169:112940. [PMID: 37254364 DOI: 10.1016/j.foodres.2023.112940] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 04/28/2023] [Accepted: 05/02/2023] [Indexed: 06/01/2023]
Abstract
This study was designed to extend the shelf life of fruits and vegetables through a novel technique based on utilization of microbially driven enzyme glucose oxidase and casting a fine layer of hydrogen peroxide on the food item that protected the fruit from decay. The produced nanoparticles (ZnO, Ag) were ligated with Glucose Oxidize (GOx) purified from Aspergillus niger. Post ligation studies revealed that ligated enzymes display relatively enhanced activity. Four types of sprays were prepared in order to compare their effectiveness. Glucose oxidase/silver nanoparticles (GOx/AgNPs), glucose oxidase/zinc oxide nanoparticles (GOx/ZnONPs), AgNPs and ZnONPs sprays were applied to guava fruit samples as post-harvest therapeutic agents for a period of 15 days. Fruit quality parameters such as total suspended solids (TSS), pH, weight loss, DPPH free radical capturing performance and firmness confirms that usage of the bioconjugates especially that of GOx/ZnONP was curiously active to maintain the physical appearance of fruit well along with no such deterioration in chemical composition of fruit. Consequently, enzymes ligated on the surface of nanoparticles (ZnONP) are exceptional for extension of post-harvest shelf life of fruits such as guava.
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Affiliation(s)
- Sumaira Shouket
- Department of Chemistry, Government College University Lahore, Lahore 54000, Pakistan
| | - Shazia Khurshid
- Department of Chemistry, Government College University Lahore, Lahore 54000, Pakistan.
| | - Jahangir Khan
- Department of Chemistry, Government College University Lahore, Lahore 54000, Pakistan
| | - Razia Batool
- Department of Forensic and Toxicology, Sahara medical college Narowal, Pakistan
| | - Abid Sarwar
- Food and Biotechnology Research Center, Pakistan Council of Scientific Industrial Research (PCSIR) Lahore, 54600, Pakistan
| | - Tariq Aziz
- School of Food & Biological Engineering, Jiangsu University Zhenjiang, 212013, China.
| | - Majid Alhomrani
- Department of Clinical Laboratory Sciences, The Faculty of Applied Medical Sciences, Taif University P.O.Box 11099, Taif 21944, Saudi Arabia
| | - Abdulhakeem S Alamri
- Department of Clinical Laboratory Sciences, The Faculty of Applied Medical Sciences, Taif University P.O.Box 11099, Taif 21944, Saudi Arabia
| | - Manal Y Sameeh
- Chemistry Department, Faculty of Applied Sciences, Al-Leith University College, Umm Al-Qura University, Makkah 24831, Saudi Arabia 6
| | - Faten Zubair Filimban
- Division of Plant Sciences, Department of Biology, King Abdulaziz University, Jeddah 21551, Saudi Arabia
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