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Gupta A, Jamal T, Rajbhar P, Gaur AS, Chauhan SS, Parthasarathi R. Cytokines inhibitory mechanism of Prunus domestica L. (Plum) peptides as potential immunomodulators against systemic lupus erythematosus: an in-silico screening. In Silico Pharmacol 2024; 12:12. [PMID: 38370860 PMCID: PMC10866836 DOI: 10.1007/s40203-023-00188-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 12/28/2023] [Indexed: 02/20/2024] Open
Abstract
Natural bioactive peptides exhibit various chemical and structural properties to enhance the immune response against multiple inflammatory and autoimmune related disorders. The immunomodulatory function and bioactivity of seed peptides show the capability for the development of biotherapeutics that could prevent autoimmune diseases. The aim of current study is to determine the immunomodulatory function of bioactive peptides derived from the seed of plum (Prunus domestica L.) by applying various immunoinformatic approaches. A thorough analysis of forty-one peptides was performed including drug likeliness, pharmacokinetic, and bioactivity profiling studies. Further, molecular docking and molecular dynamics (MD) simulations of screened peptides were carried out with the two interleukin targets (IL-17A and IL-23) of systemic lupus erythematosus (SLE). After the systematic screening, four peptides, namely HLLP, LPLL, LPAGV, and NLPL, were found as potential inhibitors against SLE. Additionally, site-directed mutagenesis analysis was conducted to explore the role of essential amino acid residues in the binding pattern/energy change. Computational alanine screening analysis found that CYS123, CYS121 of IL-17A and ASP270, and SER249 of IL-23 as hot spot residues that could play an important role in the inhibition property of screened peptides. Overall, the methodology described in the study can be utilized for developing unique peptide inhibitors that have a preventative role against SLE. Graphical abstract Supplementary Information The online version contains supplementary material available at 10.1007/s40203-023-00188-8.
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Affiliation(s)
- Anshika Gupta
- Computational Toxicology Facility, Toxicoinformatics Research Group, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhavan 31, Mahatma Gandhi Marg, Lucknow, Uttar Pradesh 226001 India
| | - Tanya Jamal
- Computational Toxicology Facility, Toxicoinformatics Research Group, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhavan 31, Mahatma Gandhi Marg, Lucknow, Uttar Pradesh 226001 India
| | - Priyanka Rajbhar
- Computational Toxicology Facility, Toxicoinformatics Research Group, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhavan 31, Mahatma Gandhi Marg, Lucknow, Uttar Pradesh 226001 India
| | - Anamika Singh Gaur
- Computational Toxicology Facility, Toxicoinformatics Research Group, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhavan 31, Mahatma Gandhi Marg, Lucknow, Uttar Pradesh 226001 India
| | - Shweta Singh Chauhan
- Computational Toxicology Facility, Toxicoinformatics Research Group, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhavan 31, Mahatma Gandhi Marg, Lucknow, Uttar Pradesh 226001 India
- Academy of Scientific and Innovative Research (AcSIR), Uttar Pradesh, Ghaziabad, 201002 India
| | - Ramakrishnan Parthasarathi
- Computational Toxicology Facility, Toxicoinformatics Research Group, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhavan 31, Mahatma Gandhi Marg, Lucknow, Uttar Pradesh 226001 India
- Academy of Scientific and Innovative Research (AcSIR), Uttar Pradesh, Ghaziabad, 201002 India
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Li H, Dong S, Duan L. Difference in the binding mechanisms of ABT-263/43b with Bcl-xL/Bcl-2: computational perspective on the accurate binding free energy analysis. J Mol Model 2021; 27:317. [PMID: 34633547 DOI: 10.1007/s00894-021-04924-9] [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: 03/18/2021] [Accepted: 09/20/2021] [Indexed: 11/26/2022]
Abstract
B-cell lymphoma/leukemia gene-2(Bcl-2) protein family known for regulating cell cycle arrest and subsequent cell death is highly expressed in a variety of cancers. Among them, the Bcl-xL and Bcl-2 are two essential proteins in the Bcl-2 family. In the present work, the differences in binding modes as between the two proteins and two ligands ABT-263/43b were investigated and compared. And the computational alanine scanning combined with the recently developed interaction entropy (AS-IE) method was employed for predicting their binding free energies and finding those amino acids that were more critical during the binding process. The result showed that the binding free energy calculated by the AS-IE method was more in line with experimental values than the molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) method. Besides, no significant difference was found between Bcl-xL and ABT-263/43b in the binding free energy, which Bcl-xL showed slightly weaker binding free energy to 43b because of the fewer number of key residues with interactions. Nonetheless, compared with the Bcl-2 and 43b complex, the Bcl-2 and ABT-263 system had greater number of key residues interacting with ABT-263, in particular, contribute favorably, resulting in a stronger binding ability for the Bcl-2 and ABT-263 systems. The van der Waals and hydrogen bond contributions were significant in the four protein-ligand complexes. Overall, Tyr108 was found to be the common key residues in the Bcl-xL-ligand complex, while Tyr105, Glu100, and Glu143 were established as the common key residue in the Bcl-2-ligand systems. We hope that the predicted hot spot residues and their energy distributions can guide the design of peptide and small-molecule drugs targeting Bcl-xL and Bcl-2.
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Affiliation(s)
- Hao Li
- Department of Science and Technology, Shandong Normal University, Jinan, 250014, China
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China
| | - Shuheng Dong
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China
| | - Lili Duan
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China.
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Sattarinezhad E, Fani N, Bordbar AK, Hatami P, Abbasi Kajani A, Taki M. Probing the physico-chemical, antioxidant and anticancer influence of β-lactoglobulin on dietary flavonoid daidzein. INFORMATICS IN MEDICINE UNLOCKED 2021. [DOI: 10.1016/j.imu.2021.100643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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Duan L, Dong S, Huang K, Cong Y, Luo S, Zhang JZH. Computational analysis of binding free energies, hotspots and the binding mechanism of Bcl-xL/Bcl-2 binding to Bad/Bax. Phys Chem Chem Phys 2021; 23:2025-2037. [DOI: 10.1039/d0cp04693k] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Hierarchical clustering tree of residues providing contributions to system binding based on the binding free energy of specific residues for (A) Bcl-xL systems (B) Bcl-2 systems.
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Affiliation(s)
- Lili Duan
- School of Physics and Electronics
- Shandong Normal University
- Jinan 250014
- China
| | - Shuheng Dong
- School of Physics and Electronics
- Shandong Normal University
- Jinan 250014
- China
| | - Kaifang Huang
- School of Physics and Electronics
- Shandong Normal University
- Jinan 250014
- China
| | - Yalong Cong
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development
- School of Chemistry and Molecular Engineering
- East China Normal University
- Shanghai
- China
| | - Song Luo
- School of Physics and Electronics
- Shandong Normal University
- Jinan 250014
- China
| | - John Z. H. Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development
- School of Chemistry and Molecular Engineering
- East China Normal University
- Shanghai
- China
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Cong Y, Duan L, Huang K, Bao J, Zhang JZH. Alanine scanning combined with interaction entropy studying the differences of binding mechanism on HIV-1 and HIV-2 proteases with inhibitor. J Biomol Struct Dyn 2020; 39:1588-1599. [DOI: 10.1080/07391102.2020.1734488] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Yalong Cong
- School of Physics and Electronics, Shandong Normal University, Jinan, China
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
| | - Lili Duan
- School of Physics and Electronics, Shandong Normal University, Jinan, China
| | - Kaifang Huang
- School of Physics and Electronics, Shandong Normal University, Jinan, China
| | - Jinxiao Bao
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
| | - John Z. H. Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, China
- Department of Chemistry, New York University, NY, NY, USA
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Dos Santos Maia M, Soares Rodrigues GC, Silva Cavalcanti AB, Scotti L, Scotti MT. Consensus Analyses in Molecular Docking Studies Applied to Medicinal Chemistry. Mini Rev Med Chem 2020; 20:1322-1340. [PMID: 32013847 DOI: 10.2174/1389557520666200204121129] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 10/31/2019] [Accepted: 11/04/2019] [Indexed: 02/08/2023]
Abstract
The increasing number of computational studies in medicinal chemistry involving molecular docking has put the technique forward as promising in Computer-Aided Drug Design. Considering the main method in the virtual screening based on the structure, consensus analysis of docking has been applied in several studies to overcome limitations of algorithms of different programs and mainly to increase the reliability of the results and reduce the number of false positives. However, some consensus scoring strategies are difficult to apply and, in some cases, are not reliable due to the small number of datasets tested. Thus, for such a methodology to be successful, it is necessary to understand why, when and how to use consensus docking. Therefore, the present study aims to present different approaches to docking consensus, applications, and several scoring strategies that have been successful and can be applied in future studies.
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Affiliation(s)
- Mayara Dos Santos Maia
- Program of Natural and Synthetic Bioactive Products (PgPNSB), Health Sciences Center, Federal University of Paraiba, Joao Pessoa-PB, Brazil
| | - Gabriela Cristina Soares Rodrigues
- Program of Natural and Synthetic Bioactive Products (PgPNSB), Health Sciences Center, Federal University of Paraiba, Joao Pessoa-PB, Brazil
| | - Andreza Barbosa Silva Cavalcanti
- Program of Natural and Synthetic Bioactive Products (PgPNSB), Health Sciences Center, Federal University of Paraiba, Joao Pessoa-PB, Brazil
| | - Luciana Scotti
- Program of Natural and Synthetic Bioactive Products (PgPNSB), Health Sciences Center, Federal University of Paraiba, Joao Pessoa-PB, Brazil
| | - Marcus Tullius Scotti
- Program of Natural and Synthetic Bioactive Products (PgPNSB), Health Sciences Center, Federal University of Paraiba, Joao Pessoa-PB, Brazil
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Shityakov S, Bigdelian E, Hussein AA, Hussain MB, Tripathi YC, Khan MU, Shariati MA. Phytochemical and pharmacological attributes of piperine: A bioactive ingredient of black pepper. Eur J Med Chem 2019; 176:149-161. [PMID: 31103896 DOI: 10.1016/j.ejmech.2019.04.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 03/16/2019] [Accepted: 04/01/2019] [Indexed: 12/11/2022]
Abstract
Plants are vital for the wellbeing of humankind in a variety of ways. Some plant extracts contain antimicrobial properties that can treat different pathogens. Most of the world's population relies on medicinal plants and natural products for their primary health care needs. Therefore, there is a growing interest in natural products, medicinal plants, and traditional medicine along with a desire to design and develop novel plant-based pharmaceuticals. These plant-based pharmaceuticals may address the concerns of reduced efficacy of synthetic antibiotics due to the emergence of drug-resistant pathogens. In this regard, some plant extracts from black pepper (Piper nigrum) with antimicrobial properties, including piperine, have the potential to be used as natural dietary supplements together with modern therapeutic approaches. This review highlights possible applications of piperine as the active compound in the fields of rational drug design and discovery, pharmaceutical chemistry, and biomedicine. We discuss different extraction methods and pharmacological effects of the analyzed substance to pave the way for further research strategies and perspectives towards the development of novel herbal products for better healthcare solutions.
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Affiliation(s)
- Sergey Shityakov
- Department of Anesthesia and Critical Care, University of Würzburg, 97080, Würzburg, Germany.
| | - Ehsan Bigdelian
- Department of Food Science and Technology, Faculty of Agricultural Engineering and Technology, University of Tehran, Iran
| | - Aqeel A Hussein
- School of Chemistry, University of Southampton, Highfield, Southampton, SO171BJ, UK; School of Medicine, University of Al-Ameed, Karbala P.O No: 198, Iraq
| | - Muhammad Bilal Hussain
- Institute of Home and Food Sciences, Government College University, Faisalabad, Pakistan
| | - Yogesh Chandra Tripathi
- Chemistry and Bioprospecting Division, Forest Research Institute, P. O. New Forest, Dehradun, 248 006, Uttarakhand, India
| | - Muhammad Usman Khan
- Bioproducts Sciences and Engineering Laboratory (BSEL), Washington State University, Richland, WA, 99354, USA; Department of Energy Systems Engineering, Faculty of Agricultural Engineering and Technology, University of Agriculture, Faisalabad, 38000, Pakistan
| | - Mohammad Ali Shariati
- Laboratory of Biocontrol and Antimicrobial Resistance, Orel State University Named After I.S. Turgenev, 302026, Orel, Russia.
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Martínez-García D, Manero-Rupérez N, Quesada R, Korrodi-Gregório L, Soto-Cerrato V. Therapeutic strategies involving survivin inhibition in cancer. Med Res Rev 2018; 39:887-909. [PMID: 30421440 DOI: 10.1002/med.21547] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Revised: 09/13/2018] [Accepted: 10/09/2018] [Indexed: 02/06/2023]
Abstract
Survivin is a small protein that belongs to the inhibitor of apoptosis protein family. It is abundantly expressed in tumors compared with adult differentiated tissues, being associated with poor prognosis in many human neoplasms. This apoptotic inhibitor has a relevant role in both the promotion of cancer cell survival and in the inhibition of cell death. Consequently, aberrant survivin expression stimulates tumor progression and confers resistance to several therapeutic strategies in a variety of tumors. In fact, efficient survivin downregulation or inhibition results in spontaneous apoptosis or sensitization to chemotherapy and radiotherapy. Therefore, all these features make survivin an attractive therapeutic target to treat cancer. Currently, there are several survivin inhibitors under clinical evaluation, although more specific and efficient survivin inhibitors are being developed. Moreover, novel combination regimens targeting survivin together with other therapeutic approaches are currently being designed and assessed. In this review, recent progress in the therapeutic options targeting survivin for cancer treatment is analyzed. Direct survivin inhibitors and their current development status are explored. Besides, the major signaling pathways implicated in survivin regulation are described and different therapeutic approaches involving survivin indirect inhibition are evaluated. Finally, promising novel inhibitors under preclinical or clinical evaluation as well as challenges of developing survivin inhibitors as a new therapy for cancer treatment are discussed.
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Affiliation(s)
- David Martínez-García
- Department of Pathology and Experimental Therapeutics, Faculty of Medicine, University of Barcelona, Barcelona, Spain.,Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Barcelona, Spain
| | - Noemí Manero-Rupérez
- Department of Pathology and Experimental Therapeutics, Faculty of Medicine, University of Barcelona, Barcelona, Spain.,Hospital del Mar Medical Research Institute, Barcelona Biomedical Research Park, Barcelona, Spain
| | - Roberto Quesada
- Department of Chemistry, Universidad de Burgos, Burgos, Spain
| | - Luís Korrodi-Gregório
- Department of Pathology and Experimental Therapeutics, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Vanessa Soto-Cerrato
- Department of Pathology and Experimental Therapeutics, Faculty of Medicine, University of Barcelona, Barcelona, Spain.,Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Barcelona, Spain
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Bera I, Marathe MV, Payghan PV, Ghoshal N. Identification of novel hits as highly prospective dual agonists for mu and kappa opioid receptors: an integrated in silico approach. J Biomol Struct Dyn 2017; 36:279-301. [DOI: 10.1080/07391102.2016.1275810] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Indrani Bera
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology , Kolkata 700032, India
| | | | - Pavan V. Payghan
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology , Kolkata 700032, India
| | - Nanda Ghoshal
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology , Kolkata 700032, India
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