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Yousaf MA, Anwer SA, Basheera S, Sivanandan S. Computational investigation of Moringa oleifera phytochemicals targeting EGFR: molecular docking, molecular dynamics simulation and density functional theory studies. J Biomol Struct Dyn 2024; 42:1901-1923. [PMID: 37154824 DOI: 10.1080/07391102.2023.2206288] [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: 12/12/2022] [Accepted: 04/08/2023] [Indexed: 05/10/2023]
Abstract
Epidermal growth factor receptor (EGFR) is a prominent target for anticancer therapy due to its role in activating several cell signaling cascades. Clinically approved EGFR inhibitors are reported to show treatment resistance and toxicity, this study, therefore, investigates Moringa oleifera phytochemicals to find potent and safe anti-EGFR compounds. For that, phytochemicals were screened based on drug-likeness and molecular docking analysis followed by molecular dynamics simulation, density functional theory analysis and ADMET analysis to identify the effective inhibitors of EGFR tyrosine kinase (EGFR-TK) domain. Known EGFR-TK inhibitors (1-4 generations) were used as control. Among 146 phytochemicals, 136 compounds showed drug-likeness, of which Delta 7-Avenasterol was the most potential EGFR-TK inhibitor with a binding energy of -9.2 kcal/mol followed by 24-Methylenecholesterol (-9.1 kcal/mol), Campesterol (-9.0 kcal/mol) and Ellagic acid (-9.0 kcal/mol). In comparison, the highest binding affinity from control drugs was displayed by Rociletinib (-9.0 kcal/mol). The molecular dynamics simulation (100 ns) exhibited the structural stability of native EGFR-TK and protein-inhibitor complexes. Further, MM/PBSA computed the binding free energies of protein complex with Delta 7-Avenasterol, 24-Methylenecholesterol, Campesterol and Ellagic acid as -154.559 ± 18.591 kJ/mol, -139.176 ± 19.236 kJ/mol, -136.212 ± 17.598 kJ/mol and -139.513 ± 23.832 kJ/mol, respectively. Non-polar interactions were the major contributors to these energies. The density functional theory analysis also established the stability of these inhibitor compounds. ADMET analysis depicted acceptable outcomes for all top phytochemicals without displaying any toxicity. In conclusion, this report has identified promising EGFR-TK inhibitors to treat several cancers that can be further investigated through laboratory and clinical tests.
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Affiliation(s)
- Muhammad Abrar Yousaf
- Section of Biology and Genetics, Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
- Department of Biology, Faculty of Science and Technology, Virtual University of Pakistan, Lahore, Pakistan
| | - Sadia Anjum Anwer
- Department of Biology, Faculty of Science and Technology, Virtual University of Pakistan, Lahore, Pakistan
| | - Shefin Basheera
- Department of Biotechnology and Bioinformatics, Saraswathy Thangavelu Extension Centre, A Research Centre of University of Kerala, KSCSTE-Jawaharlal Nehru Tropical Botanic Garden and Research Institute, Puthenthope, Thiruvananthapuram, India
| | - Sreekumar Sivanandan
- Department of Biotechnology and Bioinformatics, Saraswathy Thangavelu Extension Centre, A Research Centre of University of Kerala, KSCSTE-Jawaharlal Nehru Tropical Botanic Garden and Research Institute, Puthenthope, Thiruvananthapuram, India
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Sakthikumar K, Kabuyaya Isamura B, Krause RWM. Exploring the antioxidant, antimicrobial, cytotoxic and biothermodynamic properties of novel morpholine derivative bioactive Mn(ii), Co(ii) and Ni(ii) complexes - combined experimental and theoretical measurements towards DNA/BSA/SARS-CoV-2 3CL Pro. RSC Med Chem 2023; 14:1667-1697. [PMID: 37731703 PMCID: PMC10508264 DOI: 10.1039/d2md00394e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 12/07/2022] [Indexed: 09/22/2023] Open
Abstract
A novel class of bioactive complexes (1-3) [MII(L)2(bpy)], where, L = 2-(4-morpholinobenzylideneamino)phenol, bpy = 2,2'-bipyridine, MII = Mn (1), Co (2) or Ni (3), were assigned to octahedral geometry based on analytical and spectral measurements. Gel electrophoresis showed that complex (2) demonstrated significant DNA cleavage activity compared to the other complexes under the action of oxidation agent (H2O2). The DNA binding constant properties measured by various techniques were in the following sequence: (2) > (3) > (1) > (HL), which suggests that the complexes might intercalate DNA, a possibility that is also supported by their biothermodynamic characteristics. The binding constant results for BSA from electronic absorption and fluorometric titrations demonstrate that complex (2) exhibits the highest binding effectiveness among them all, which means that all the compounds could interact with BSA through a static approach, additionally supported by FRET measurements. DFT and docking calculations were employed to realize the electronic structure, reactivity, and interaction capability of all substances with DNA, BSA, and the SARS-CoV-2 main protease. These binding energies fell within the ranges -7.7 to -8.5, -8.2 to -10.1 and -6.7 to -9.3 kcal mol-1, respectively. The higher reactivity of the complexes than the ligand is supported by FMO theory. The in vitro antibacterial, cytotoxicity, and radical scavenging characteristics revealed that complexes (2-3) have better biological efficacy than the others. The cytotoxicity and binding properties also show good correlation with the partition coefficient (log P), which is encouraging because all of the experimental findings are closely correlated with the theoretical measurements.
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Affiliation(s)
- Karunganathan Sakthikumar
- Organic & Medicinal Chemistry, Department of Chemistry, Center for Chemico- and Biomedicinal Research (CCBR), Faculty of Science, Rhodes University Grahamstown 6140 Eastern Cape South Africa
| | - Bienfait Kabuyaya Isamura
- Organic & Medicinal Chemistry, Department of Chemistry, Center for Chemico- and Biomedicinal Research (CCBR), Faculty of Science, Rhodes University Grahamstown 6140 Eastern Cape South Africa
- Department of Chemistry, The University of Manchester Manchester M13 9PL UK
| | - Rui Werner Maçedo Krause
- Organic & Medicinal Chemistry, Department of Chemistry, Center for Chemico- and Biomedicinal Research (CCBR), Faculty of Science, Rhodes University Grahamstown 6140 Eastern Cape South Africa
- Center for Chemico- and Biomedicinal Research (CCBR), Faculty of Science, Rhodes University Grahamstown 6140 Eastern Cape South Africa +27 741622674 +27 46 603 7030
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Chavda VP, Valu DD, Parikh PK, Tiwari N, Chhipa AS, Shukla S, Patel SS, Balar PC, Paiva-Santos AC, Patravale V. Conventional and Novel Diagnostic Tools for the Diagnosis of Emerging SARS-CoV-2 Variants. Vaccines (Basel) 2023; 11:vaccines11020374. [PMID: 36851252 PMCID: PMC9960989 DOI: 10.3390/vaccines11020374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/25/2023] [Accepted: 02/02/2023] [Indexed: 02/10/2023] Open
Abstract
Accurate identification at an early stage of infection is critical for effective care of any infectious disease. The "coronavirus disease 2019 (COVID-19)" outbreak, caused by the virus "Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)", corresponds to the current and global pandemic, characterized by several developing variants, many of which are classified as variants of concern (VOCs) by the "World Health Organization (WHO, Geneva, Switzerland)". The primary diagnosis of infection is made using either the molecular technique of RT-PCR, which detects parts of the viral genome's RNA, or immunodiagnostic procedures, which identify viral proteins or antibodies generated by the host. As the demand for the RT-PCR test grew fast, several inexperienced producers joined the market with innovative kits, and an increasing number of laboratories joined the diagnostic field, rendering the test results increasingly prone to mistakes. It is difficult to determine how the outcomes of one unnoticed result could influence decisions about patient quarantine and social isolation, particularly when the patients themselves are health care providers. The development of point-of-care testing helps in the rapid in-field diagnosis of the disease, and such testing can also be used as a bedside monitor for mapping the progression of the disease in critical patients. In this review, we have provided the readers with available molecular diagnostic techniques and their pitfalls in detecting emerging VOCs of SARS-CoV-2, and lastly, we have discussed AI-ML- and nanotechnology-based smart diagnostic techniques for SARS-CoV-2 detection.
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Affiliation(s)
- Vivek P. Chavda
- Department of Pharmaceutics and Pharmaceutical Technology, L. M. College of Pharmacy, Ahmedabad 380009, Gujarat, India
- Correspondence: (V.P.C.); or (V.P.)
| | - Disha D. Valu
- Formulation and Drug Product Development, Biopharma Division, Intas Pharmaceutical Ltd., 3000-548 Moraiya, Ahmedabad 380054, Gujarat, India
| | - Palak K. Parikh
- Department of Pharmaceutical Chemistry and Quality Assurance, L. M. College of Pharmacy, Ahmedabad 380009, Gujarat, India
| | - Nikita Tiwari
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai 400019, Maharashtra, India
| | - Abu Sufiyan Chhipa
- Department of Pharmacology, Institute of Pharmacy, Nirma University, Ahmedabad 382481, Gujarat, India
| | - Somanshi Shukla
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai 400019, Maharashtra, India
| | - Snehal S. Patel
- Department of Pharmacology, Institute of Pharmacy, Nirma University, Ahmedabad 382481, Gujarat, India
| | - Pankti C. Balar
- Pharmacy Section, L. M. College of Pharmacy, Ahmedabad 380009, Gujarat, India
| | - Ana Cláudia Paiva-Santos
- Department of Pharmaceutical Technology, Faculty of Pharmacy of the University of Coimbra, University of Coimbra, 3000-548 Coimbra, Portugal
- REQUIMTE/LAQV, Group of Pharmaceutical Technology, Faculty of Pharmacy of the University of Coimbra, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Vandana Patravale
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai 400019, Maharashtra, India
- Correspondence: (V.P.C.); or (V.P.)
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Bezbaruah R, Chavda VP, Nongrang L, Alom S, Deka K, Kalita T, Ali F, Bhattacharjee B, Vora L. Nanoparticle-Based Delivery Systems for Vaccines. Vaccines (Basel) 2022; 10:vaccines10111946. [PMID: 36423041 PMCID: PMC9694785 DOI: 10.3390/vaccines10111946] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 11/08/2022] [Accepted: 11/09/2022] [Indexed: 11/19/2022] Open
Abstract
Vaccination is still the most cost-effective way to combat infectious illnesses. Conventional vaccinations may have low immunogenicity and, in most situations, only provide partial protection. A new class of nanoparticle-based vaccinations has shown considerable promise in addressing the majority of the shortcomings of traditional and subunit vaccines. This is due to recent breakthroughs in chemical and biological engineering, which allow for the exact regulation of nanoparticle size, shape, functionality, and surface characteristics, resulting in improved antigen presentation and robust immunogenicity. A blend of physicochemical, immunological, and toxicological experiments can be used to accurately characterize nanovaccines. This narrative review will provide an overview of the current scenario of the nanovaccine.
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Affiliation(s)
- Rajashri Bezbaruah
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh 786004, Assam, India
| | - Vivek P. Chavda
- Department of Pharmaceutics and Pharmaceutical Technology, L. M. College of Pharmacy, Ahmedabad 380008, Gujarat, India
- Correspondence:
| | - Lawandashisha Nongrang
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh 786004, Assam, India
| | - Shahnaz Alom
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh 786004, Assam, India
- Department of Pharmacology, Girijananda Chowdhury Institute of Pharmaceutical Science-Tezpur, Sonitpur 784501, Assam, India
| | - Kangkan Deka
- Department of Pharmacognosy, NETES Institute of Pharmaceutical Science, Mirza, Guwahati 781125, Assam, India
| | - Tutumoni Kalita
- Department of Pharmaceutical Chemistry, Girijananda Chowdhury Institute of Pharmaceutical Sciences, Azara, Guwahati 781017, Assam, India
| | - Farak Ali
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh 786004, Assam, India
- Department of Pharmaceutical Chemistry, Girijananda Chowdhury Institute of Pharmaceutical Science-Tezpur, Sonitpur 784501, Assam, India
| | - Bedanta Bhattacharjee
- Department of Pharmacology, Girijananda Chowdhury Institute of Pharmaceutical Science-Tezpur, Sonitpur 784501, Assam, India
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