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Nascimento IJDS, Cavalcanti MDAT, de Moura RO. Exploring N-myristoyltransferase as a promising drug target against parasitic neglected tropical diseases. Eur J Med Chem 2023; 258:115550. [PMID: 37336067 DOI: 10.1016/j.ejmech.2023.115550] [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: 05/15/2023] [Revised: 06/04/2023] [Accepted: 06/06/2023] [Indexed: 06/21/2023]
Abstract
Neglected tropical diseases (NTDs) constitute a group of approximately 20 infectious diseases that mainly affect the impoverished population without basic sanitation in tropical countries. These diseases are responsible for many deaths worldwide, costing billions of dollars in public health investment to treat and control these infections. Among them are the diseases caused by protozoa of the Trypanosomatid family, which constitute Trypanosoma cruzi (Chagas disease), Trypanosoma brucei (sleeping sickness), and Leishmaniasis. In addition, there is a classification of other diseases, called the big three, AIDS, tuberculosis, and malaria, which are endemic in countries with tropical conditions. Despite the high mortality rates, there is still a gap in the treatment. The drugs have a high incidence of side effects and protozoan resistance, justifying the investment in developing new alternatives. In fact, the Target-Based Drug Design (TBDD) approach is responsible for identifying several promising compounds, and among the targets explored through this approach, N-myristoyltransferase (NMT) stands out. It is an enzyme related to the co-translational myristoylation of N-terminal glycine in various peptides. The myristoylation process is a co-translation that occurs after removing the initiator methionine. This process regulates the assembly of protein complexes and stability, which justifies its potential as a drug target. In order to propose NMT as a potential target for parasitic diseases, this review will address the entire structure and function of this enzyme and the primary studies demonstrating its promising potential against Leishmaniasis, T. cruzi, T. brucei, and malaria. We hope our information can help researchers worldwide search for potential drugs against these diseases that have been threatening the health of the world's population.
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Affiliation(s)
- Igor José Dos Santos Nascimento
- Postgraduate Program in Pharmaceutical Sciences, State University of Paraíba, Campina Grande, 58429-500, Brazil; Cesmac University Center, Pharmacy Departament, Maceió, Brazil; Drug Development and Synthesis Laboratory, Department of Pharmacy, State University of Paraíba, Campina Grande, 58429-500, Brazil.
| | - Misael de Azevedo Teotônio Cavalcanti
- Postgraduate Program in Pharmaceutical Sciences, State University of Paraíba, Campina Grande, 58429-500, Brazil; Drug Development and Synthesis Laboratory, Department of Pharmacy, State University of Paraíba, Campina Grande, 58429-500, Brazil
| | - Ricardo Olimpio de Moura
- Postgraduate Program in Pharmaceutical Sciences, State University of Paraíba, Campina Grande, 58429-500, Brazil; Drug Development and Synthesis Laboratory, Department of Pharmacy, State University of Paraíba, Campina Grande, 58429-500, Brazil
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Design, molecular docking, and molecular dynamics of thiourea-iron (III) metal complexes as NUDT5 inhibitors for breast cancer treatment. Heliyon 2022; 8:e10694. [PMID: 36177227 PMCID: PMC9513778 DOI: 10.1016/j.heliyon.2022.e10694] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 07/02/2022] [Accepted: 09/14/2022] [Indexed: 11/29/2022] Open
Abstract
In research, anticancer agents, such as thiourea derivative compounds, and metal complexes, such as those complexed with iron (III) metal, are often studied. The metal complexes are presumably more active than thiourea derivatives as free ligands; some negative effects may be reduced. The computational studies used in this study involved molecular docking with AutoDock and molecular dynamics (MD) simulations using Desmond to evaluate the stability of the interactions. The docking and MD analysis results showed that compounds 2 and 6 had stable interactions with NUDIX hydrolase type 5 (NUDT5)—one of the therapeutic targets for breast cancer—where they had the lowest root mean square deviation (RMSD) and root mean square fluctuation (RMSF) values compared to the other compounds. Together, these compounds are anti-breast cancer drug candidates.
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Ibezim A, Onuku R, Ottih C, Ezeonu I, Onoabedje E, Ramanathan K, Nwodo N. New sulphonamide-peptide hybrid molecules as potential PBP 2a ligands and methicillin resistant Staphylococcus aureus actives. J Biomol Struct Dyn 2022:1-11. [PMID: 35975581 DOI: 10.1080/07391102.2022.2111359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
Penicillin binding protein 2a (PbP 2a) expression accounts for the insusceptibility of methicillin-resistant Staphylocuccus aureus (MRSA) to β-lactam antibiotics. Here we employed computational strategies to challenge PbP 2a with series of fifty-five 'ala-ala' and 'ala-pro' sulphonamide-dipeptides. Binding stability of two compounds (labeled: 10i and 10n) with theoretical Ki in nM and µM ranges, for PbP 2a active and allosteric sites respectively, were investigated using molecular dynamics simulations. In addition, the results of the sensitivity of four strains of MRSA for compounds 10i and 10n obtained revealed the compounds at 10 µg/ml caused two isolates (S4 and S10) to revert to being susceptible. Finally, a reliable binding conformations of both compounds in the two binding sites of PbP 2a are described to provide rationale for structure-activity optimization of this series.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Akachukwu Ibezim
- Department of Pharmaceutical and Medicinal Chemistry, University of Nigeria, Nsukka, Nigeria.,Department of Biotechnology, Vellore Institute of Technology, Vellore, Tamilnadu, India
| | - Raphael Onuku
- Department of Pharmaceutical and Medicinal Chemistry, University of Nigeria, Nsukka, Nigeria
| | - Chidalu Ottih
- Department of Microbiology, University of Nigeria, Nsukka, Nigeria
| | - Ifeoma Ezeonu
- Department of Microbiology, University of Nigeria, Nsukka, Nigeria
| | - Efeturi Onoabedje
- Department of Pure and Industrial Chemistry, University of Nigeria, Nsukka, Nigeria
| | | | - Ngozi Nwodo
- Department of Pharmaceutical and Medicinal Chemistry, University of Nigeria, Nsukka, Nigeria
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An Overview of NRF2-Activating Compounds Bearing α,β-Unsaturated Moiety and Their Antioxidant Effects. Int J Mol Sci 2022; 23:ijms23158466. [PMID: 35955599 PMCID: PMC9369284 DOI: 10.3390/ijms23158466] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 07/25/2022] [Accepted: 07/27/2022] [Indexed: 02/05/2023] Open
Abstract
The surge of scientific interest in the discovery of Nuclear Factor Erythroid 2 (NFE2)-Related Factor 2 (NRF2)-activating molecules underscores the importance of NRF2 as a therapeutic target especially for oxidative stress. The chemical reactivity and biological activities of several bioactive compounds have been linked to the presence of α,β-unsaturated structural systems. The α,β-unsaturated carbonyl, sulfonyl and sulfinyl functional groups are reportedly the major α,β-unsaturated moieties involved in the activation of the NRF2 signaling pathway. The carbonyl, sulfonyl and sulfinyl groups are generally electron-withdrawing groups, and the presence of the α,β-unsaturated structure qualifies them as suitable electrophiles for Michael addition reaction with nucleophilic thiols of cysteine residues within the proximal negative regulator of NRF2, Kelch-like ECH-associated protein 1 (KEAP1). The physicochemical property such as good lipophilicity of these moieties is also an advantage because it ensures solubility and membrane permeability required for the activation of the cytosolic NRF2/KEAP1 system. This review provides an overview of the reaction mechanism of α,β-unsaturated moiety-bearing compounds with the NRF2/KEAP1 complex, their pharmacological properties, structural activity-relationship and their effect on antioxidant and anti-inflammatory responses. As the first of its kind, this review article offers collective and comprehensive information on NRF2-activators containing α,β-unsaturated moiety with the aim of broadening their therapeutic prospects in a wide range of oxidative stress-related diseases.
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Fragment-based virtual screening discovers potential new Plasmodium PI4KIIIβ ligands. BMC Chem 2022; 16:19. [PMID: 35331319 PMCID: PMC8944149 DOI: 10.1186/s13065-022-00812-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 03/07/2022] [Indexed: 12/17/2022] Open
Abstract
Type III beta phosphatidylinositol 4-kinase (PI4KIIIβ) is the only clinically validated drug target in Plasmodium kinases and therefore a critical target in developing novel drugs for malaria. Current PI4KIIIβ inhibitors have solubility and off-target problems. Here we set out to identify new Plasmodium PI4K ligands that could serve as leads for the development of new antimalarial drugs by building a PPI4K homology model since there was no available three-dimensional structure of PfPI4K and virtually screened a small library of ~ 22 000 fragments against it. Sixteen compounds from the fragment-based virtual screening (FBVS) were selected based on ≤ − 9.0 kcal/mol binding free energy cut-off value. These were subjected to similarity and sub-structure searching after they had passed PAINS screening and the obtained derivatives showed improved binding affinity for PfPI4K (− 10.00 to − 13.80 kcal/mol). Moreover, binding hypothesis of the top-scoring compound (31) was confirmed in a 100 ns molecular dynamics simulation and its binding pose retrieved after the system had converged at about 10 ns into the evolution was described to lay foundation for a rationale chemical-modification to optimize binding to PfPI4K. Overall, compound 31 appears to be a viable starting point for the development of PPI4K inhibitors with antimalarial activity.
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Rational drug design, synthesis, and biological evaluation of novel N-(2-arylaminophenyl)-2,3-diphenylquinoxaline-6-sulfonamides as potential antimalarial, antifungal, and antibacterial agents. DIGITAL CHINESE MEDICINE 2021. [DOI: 10.1016/j.dcmed.2021.12.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Ibezim A, Onuku RS, Ibezim A, Ntie-Kang F, Nwodo NJ, Adikwu MU. Structure-based virtual screening and molecular dynamics simulation studies to discover new SARS-CoV-2 main protease inhibitors. SCIENTIFIC AFRICAN 2021; 14:e00970. [PMID: 34541426 PMCID: PMC8438860 DOI: 10.1016/j.sciaf.2021.e00970] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 08/13/2021] [Accepted: 09/09/2021] [Indexed: 12/12/2022] Open
Abstract
Computational methods were used to filter two datasets (> 8,000 compounds) based on two criteria: higher binding affinity for MPRO than cocrystallized inhibitor and binding interactions with MPRO catalytic dyad (Cys145 and His41). After virtual screening involving ranking and reranking, eleven compounds were identified to satisfy these criteria and analysis of their structures revealed an unparallel common features among them which could be critical for their interactions with MPRO. However, only the topmost scoring compound (AV-203: Ki = 0.31 µM) exhibited relatively stable binding interaction during the period of 50 ns MD simulation and thus is a suitable template for drug development.
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Affiliation(s)
- A Ibezim
- Department of Pharmaceutical and Medicinal Chemistry, Faculty of Pharmaceutical Sciences, University of Nigeria, Nsukka, Nigeria
| | - R S Onuku
- Department of Pharmaceutical and Medicinal Chemistry, Faculty of Pharmaceutical Sciences, University of Nigeria, Nsukka, Nigeria
| | - A Ibezim
- Information and Communication Technology Unit, University of Nigeria, Nsukka, Nigeria
| | - F Ntie-Kang
- Department of Chemistry, Faculty of Science, University of Buea, P. O. Box 63, Buea, Cameroon.,Institute for Pharmacy, Martin-Luther-Universität Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120 Halle (Saale), Germany.,Institute of Botany, Technical University of Dresden, Zellescher Weg 20b, 01217 Dresden, Germany
| | - N J Nwodo
- Department of Pharmaceutical and Medicinal Chemistry, Faculty of Pharmaceutical Sciences, University of Nigeria, Nsukka, Nigeria
| | - M U Adikwu
- Department of Pharmaceutical Microbiology and Biopharmaceutics, Faculty of Pharmaceutical Sciences, University of Nigeria, Nsukka, Nigeria
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Asdaq SMB, Swathi E, Dhamanigi SS, Asad M, Ali Mohzari Y, Alrashed AA, Alotaibi AS, Mohammed Alhassan B, Nagaraja S. Role of Daucus carota in Enhancing Antiulcer Profile of Pantoprazole in Experimental Animals. MOLECULES (BASEL, SWITZERLAND) 2020; 25:molecules25225287. [PMID: 33202703 PMCID: PMC7696376 DOI: 10.3390/molecules25225287] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 10/30/2020] [Accepted: 11/09/2020] [Indexed: 12/25/2022]
Abstract
The carrot plant (Daucus carota) and its components are traditionally reported for the management of gastric ulcers. This study was performed to evaluate the role of carrot when administered concurrently with a conventional antiulcer treatment, pantoprazole, in alleviating gastric and duodenal ulcers in female experimental animals. The study involved standard animal models to determine the ulcer preventive effect using pylorus ligation, ethanol, and stress induced acute gastric ulcer models and duodenal ulcer models involving cysteamine. Acetic acid-induced chronic gastric ulcer and indomethacin-induced gastric ulcer models were used to evaluate the ulcer healing effect. Carrot fruit (500 mg/kg) and its co-administration with pantoprazole produced significant protection in an ethanol- and stress-induced acute gastric ulcer and cysteamine-induced duodenal ulcer. The healing of the acetic acid-induced chronic gastric ulcer was also augmented with this combination. Both total proteins and mucin contents were significantly increased in indomethacin-induced gastric ulcers. Similarly, in pylorus ligation, the pepsin content of gastric juice, total acidity, and free acidity were reduced. Overall, both ulcer preventive effects and ulcer healing properties of the pantoprazole were significantly enhanced in animals who received the co-administration of carrot fruit (500 mg/kg).
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Affiliation(s)
- Syed Mohammed Basheeruddin Asdaq
- Department of Pharmacology, College of Pharmacy, AlMaarefa University, Riyadh 13713, Saudi Arabia
- Correspondence: ; Tel.: +966-1-403555-3399
| | - Earla Swathi
- Department of Pharmacology, Krupanidhi College of Pharmacy, Bangalore 560035, India; (E.S.); (S.S.D.)
| | - Sunil S Dhamanigi
- Department of Pharmacology, Krupanidhi College of Pharmacy, Bangalore 560035, India; (E.S.); (S.S.D.)
| | - Mohammed Asad
- College of Applied Medical Sciences, Shaqra University, Shaqra 11911, Saudi Arabia;
| | - Yahya Ali Mohzari
- Clinical Pharmacy Department, King Saud Medical City, Riyadh 12746, Saudi Arabia;
| | - Ahmed A. Alrashed
- Pharmaceutical Service Department, Inpatient Pharmacy, King Fahad Medical City, Riyadh 11525, Saudi Arabia; (A.A.A.); (A.S.A.)
| | - Abdulrahman S. Alotaibi
- Pharmaceutical Service Department, Inpatient Pharmacy, King Fahad Medical City, Riyadh 11525, Saudi Arabia; (A.A.A.); (A.S.A.)
| | | | - Sreeharsha Nagaraja
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Saudi Arabia;
- Department of Pharmaceutics, Vidya Siri College of Pharmacy, Off Sarjapura Road, Bangalore 560035, India
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