1
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Saha D, Jha AN. Integrated subtractive genomics and structure-based approach to unravel the therapeutic drug target of Leishmania species. Arch Microbiol 2024; 206:408. [PMID: 39299989 DOI: 10.1007/s00203-024-04118-w] [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: 05/22/2024] [Revised: 08/23/2024] [Accepted: 08/25/2024] [Indexed: 09/22/2024]
Abstract
Leishmaniasis is a complex vector-borne disease caused by intracellular protozoan parasites of the Leishmania genus. It presents a significant public health challenge in tropical and subtropical regions globally. As resistance to treatment increases, managing and controlling Leishmaniasis becomes more challenging, necessitating innovative approaches. To address this challenge, our study utilized subtractive genomics and structure-based approaches to identify common drug targets and combat antimicrobial resistance (AMR) across five Leishmania species strains. The subtractive genomics approach unraveled Glutamate Dehydrogenase (GDH) as a promising drug target for treating Leishmania infections. The investigation considered established methodologies observed in analogous studies, orthologous group, and druggability tests. Multiple sequence alignment revealed conserved sequences in GDH, while phylogenetic tree analysis provided insights into the evolutionary origin and close relationships of GDH across Leishmania species. Conserved sequences in GDH along with its function in pathogenicity provided insights into the close relationships of GDH across Leishmania species. Using a structure-based approach, our study showed the molecular interactions between GDH and three ligands-Bithionol, GW5074, and Hexachlorophene-through molecular docking and 100 ns molecular dynamics (MD) simulations. GW5074 exhibited a significant affinity for GDH, as indicated by stable RMSD values, a more compact conformation, and a higher number of hydrogen bonds than Bithionol. MMPBSA analysis confirmed the superior binding energy of the GW5074-GDH complex, emphasizing its potential as a potent ligand for drug development. This comprehensive analysis identified GW5074 as a promising candidate for inhibiting GDH activities in Leishmania species, contributing to the development of effective therapeutics against Leishmania infections.
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Affiliation(s)
- Debanjan Saha
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, India
| | - Anupam Nath Jha
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, India.
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2
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Balkrishna A, Sharma Y, Dabas S, Arya V, Dabas A. Molecular Mechanism of Cynodon dactylon Phytosterols Targeting MAPK3 and PARP1 to Combat Epithelial Ovarian Cancer: A Multifaceted Computational Approach. Cell Biochem Biophys 2024; 82:2625-2650. [PMID: 38961033 DOI: 10.1007/s12013-024-01375-w] [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] [Accepted: 06/18/2024] [Indexed: 07/05/2024]
Abstract
Epithelial Ovarian Cancer (EOC) presents a global health concern, necessitating the development of innovative therapeutic strategies to combat its impact. This study was employed to investigate the unexplored therapeutic efficacy of Cynodon dactylon phytochemicals against EOC using a multifaceted computational approach. A total of 19 out of 89 rigorously curated phytochemicals were assessed as potential drug targets via ADMET profiling, while protein-protein interaction analysis scrutinized the top 20 hub genes among 264 disease targets, revealing their involvement in cancer-related pathways and underscoring their significance in EOC pathogenesis. In molecular docking, Stigmasterol acetate showed the highest binding affinity (-10.9 kcal/mol) with Poly [ADP-ribose] polymerase-1 (PDB: 1UK1), while Arundoin and Beta-Sitosterol exhibited strong affinities (-10.4 kcal/mol and -10.1 kcal/mol, respectively); additionally, Beta-Sitosterol interacting with Mitogen-activated protein kinase 3 (PDB: 4QTB) showed a binding affinity of -10.1 kcal/mol, forming 2 hydrogen bonds and a total of 10 bonds with 10 residues. Molecular dynamics simulations exhibited the significant structural stability of the Beta-Sitosterol-4QTB complex with superior binding free energy (-36.61 kcal/mol) among the three complexes. This study identified C. dactylon phytosterols, particularly Beta-Sitosterol, as effective in targeting MAPK3 and PARP1 to combat EOC, laying the groundwork for further experimental validation and drug development efforts.
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Affiliation(s)
- Acharya Balkrishna
- Patanjali Herbal Research Department, Patanjali Research Foundation, Haridwar, 249405, Uttarakhand, India
- University of Patanjali, Patanjali Yogpeeth, Haridwar, 249405, Uttarakhand, India
| | - Yoganshi Sharma
- Patanjali Herbal Research Department, Patanjali Research Foundation, Haridwar, 249405, Uttarakhand, India
| | - Shakshi Dabas
- Patanjali Herbal Research Department, Patanjali Research Foundation, Haridwar, 249405, Uttarakhand, India
| | - Vedpriya Arya
- Patanjali Herbal Research Department, Patanjali Research Foundation, Haridwar, 249405, Uttarakhand, India
- University of Patanjali, Patanjali Yogpeeth, Haridwar, 249405, Uttarakhand, India
| | - Anurag Dabas
- Patanjali Herbal Research Department, Patanjali Research Foundation, Haridwar, 249405, Uttarakhand, India.
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3
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Haider S, Shafiq M, Siddiqui AR, Sardar M, Mushtaq M, Shafeeq S, Nur-E-Alam M, Ahmad A, Ul-Haq Z. Uncovering PPAR-γ agonists: An integrated computational approach driven by machine learning. J Mol Graph Model 2024; 129:108742. [PMID: 38422823 DOI: 10.1016/j.jmgm.2024.108742] [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: 10/16/2023] [Revised: 02/16/2024] [Accepted: 02/16/2024] [Indexed: 03/02/2024]
Abstract
Peroxisome proliferator-activated receptor gamma (PPAR-γ) serves as a nuclear receptor with a pivotal function in governing diverse facets of metabolic processes. In diabetes, the prime physiological role of PPAR-γ is to enhance insulin sensitivity and regulate glucose metabolism. Although PPAR-γ agonists such as Thiazolidinediones are effective in addressing diabetes complications, it is vital to be mindful that they are associated with substantial side effects that could potentially give rise to health challenges. The recent surge in the discovery of selective modulators of PPAR-γ inspired us to formulate an integrated computational strategy by leveraging the promising capabilities of both machine learning and in silico drug design approaches. In pursuit of our objectives, the initial stage of our work involved constructing an advanced machine learning classification model, which was trained utilizing chemical information and physicochemical descriptors obtained from known PPAR-γ modulators. The subsequent application of machine learning-based virtual screening, using a library of 31,750 compounds, allowed us to identify 68 compounds having suitable characteristics for further investigation. A total of four compounds were identified and the most favorable configurations were complemented with docking scores ranging from -8.0 to -9.1 kcal/mol. Additionally, the compounds engaged in hydrogen bond interactions with essential conserved residues including His323, Leu330, Phe363, His449 and Tyr473 that describe the ligand binding site. The stability indices investigated herein for instance root-mean-square fluctuations in the backbone atoms indicated higher mobility in the region of orthosteric site in the presence of agonist with the deviation peaks in the range of 0.07-0.69 nm, signifying moderate conformational changes. The deviations at global level revealed that the average values lie in the range of 0.25-0.32 nm. In conclusion, our identified hits particularly, CHEMBL-3185642 and CHEMBL-3554847 presented outstanding results and highlighted the stable conformation within the orthosteric site of PPAR-γ to positively modulate the activity.
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Affiliation(s)
- Sajjad Haider
- H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Muhammad Shafiq
- H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Ali Raza Siddiqui
- H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Madiha Sardar
- H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Mamona Mushtaq
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Sehrish Shafeeq
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Mohammad Nur-E-Alam
- Department of Pharmacognosy, College of Pharmacy, King Saud University, P.O. Box. 2457, Riyadh, 11451, Kingdom of Saudi Arabia
| | - Aftab Ahmad
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA, 92618, USA
| | - Zaheer Ul-Haq
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan.
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4
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Zare F, Ataollahi E, Mardaneh P, Sakhteman A, Keshavarz V, Solhjoo A, Emami L. A combination of virtual screening, molecular dynamics simulation, MM/PBSA, ADMET, and DFT calculations to identify a potential DPP4 inhibitor. Sci Rep 2024; 14:7749. [PMID: 38565703 PMCID: PMC10987597 DOI: 10.1038/s41598-024-58485-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 03/29/2024] [Indexed: 04/04/2024] Open
Abstract
DPP4 inhibitors can control glucose homeostasis by increasing the level of GLP-1 incretins hormone due to dipeptidase mimicking. Despite the potent effects of DPP4 inhibitors, these compounds cause unwanted toxicity attributable to their effect on other enzymes. As a result, it seems essential to find novel and DPP4 selective compounds. In this study, we introduce a potent and selective DPP4 inhibitor via structure-based virtual screening, molecular docking, molecular dynamics simulation, MM/PBSA calculations, DFT analysis, and ADMET profile. The screened compounds based on similarity with FDA-approved DPP4 inhibitors were docked towards the DPP4 enzyme. The compound with the highest docking score, ZINC000003015356, was selected. For further considerations, molecular docking studies were performed on selected ligands and FDA-approved drugs for DPP8 and DPP9 enzymes. Molecular dynamics simulation was run during 200 ns and the analysis of RMSD, RMSF, Rg, PCA, and hydrogen bonding were performed. The MD outputs showed stability of the ligand-protein complex compared to available drugs in the market. The total free binding energy obtained for the proposed DPP4 inhibitor was more negative than its co-crystal ligand (N7F). ZINC000003015356 confirmed the role of the five Lipinski rule and also, have low toxicity parameter according to properties. Finally, DFT calculations indicated that this compound is sufficiently soft.
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Affiliation(s)
- Fateme Zare
- Department of Medicinal Chemistry, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Elaheh Ataollahi
- Department of Medicinal Chemistry, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Pegah Mardaneh
- Department of Medicinal Chemistry, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Amirhossein Sakhteman
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), 85354, Freising, Germany
| | - Valiollah Keshavarz
- Department of Medicinal Chemistry, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Aida Solhjoo
- Department of Quality Control of Drug Products, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Leila Emami
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
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Rahman MS, Hosen ME, Faruqe MO, Khalekuzzaman M, Islam MA, Acharjee UK, Bin Jardan YA, Nafidi HA, Mekonnen AB, Bourhia M, Zaman R. Evaluation of Adenanthera pavonina-derived compounds against diabetes mellitus: insight into the phytochemical analysis and in silico assays. Front Mol Biosci 2024; 10:1278701. [PMID: 38601799 PMCID: PMC11004346 DOI: 10.3389/fmolb.2023.1278701] [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: 08/16/2023] [Accepted: 12/19/2023] [Indexed: 04/12/2024] Open
Abstract
Adenanthera pavonina is a medicinal plant with numerous potential secondary metabolites showing a significant level of antidiabetic activity. The objective of the current study was to identify potential phytochemicals from the methanolic leaf extract of Adenanthera pavonina as therapeutic agents against diabetes mellitus using GC-MS and in silico methods. The GC-MS analysis of the leaf extract revealed a total of 17 phytochemicals. Molecular docking was performed using these phytochemicals, targeting the mutated insulin receptor tyrosine kinase (5hhw), which inhibits glucose uptake by cells. Diazoprogesterone (-9.2 kcal/mol), 2,4,4,7a-Tetramethyl-1-(3-oxobutyl)octahydro-1H-indene-2-carboxylic acid (-6.9 kcal/mol), and 2-Naphthalenemethanol, decahydro-.alpha.,.alpha.,4a-trimethyl-8-methylene-, [2R-(2.alpha.,4a.alpha.,8a.beta.)] (-6.6 kcal/mol) exhibited better binding with the target protein. The ADMET analysis was performed for the top three compounds with the best docking scores, which showed positive results with no observed toxicity in the AMES test. Furthermore, the molecular dynamics study confirmed the favorable binding of Diazoprogesterone, 2,4,4,7a-Tetramethyl-1-(3-oxobutyl)octahydro-1H-indene-2-carboxylic acid and 2-Naphthalenemethanol, decahydro-.alpha.,.alpha.,4a-trimethyl-8-methylene-, [2R-(2.alpha.,4a.alpha.,8a.beta.)] with the receptor throughout the 100 ns simulation period.
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Affiliation(s)
- Md. Sojiur Rahman
- Professor Joarder DNA and Chromosome Research Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Md. Eram Hosen
- Professor Joarder DNA and Chromosome Research Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Md. Omar Faruqe
- Department of Computer Science and Engineering, University of Rajshahi, Rajshahi, Bangladesh
| | - Md. Khalekuzzaman
- Professor Joarder DNA and Chromosome Research Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Md. Asadul Islam
- Professor Joarder DNA and Chromosome Research Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Uzzal Kumar Acharjee
- Professor Joarder DNA and Chromosome Research Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Yousef A. Bin Jardan
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Hiba-Allah Nafidi
- Department of Food Science, Faculty of Agricultural and Food Sciences, Laval University, Quebec City, QC, Canada
| | | | - Mohammed Bourhia
- Laboratory of Biotechnology and Natural Resources Valorization, Faculty of Sciences, Ibn Zohr University, Agadir, Morocco
| | - Rashed Zaman
- Professor Joarder DNA and Chromosome Research Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
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Jawarkar RD, Zaki MEA, Al-Hussain SA, Al-Mutairi AA, Samad A, Masand V, Humane V, Mali S, Alzahrani AYA, Rashid S, Elossaily GM. Mechanistic QSAR modeling derived virtual screening, drug repurposing, ADMET and in- vitro evaluation to identify anticancer lead as lysine-specific demethylase 5a inhibitor. J Biomol Struct Dyn 2024:1-31. [PMID: 38385447 DOI: 10.1080/07391102.2024.2319104] [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: 08/24/2023] [Accepted: 02/11/2024] [Indexed: 02/23/2024]
Abstract
A lysine-specific demethylase is an enzyme that selectively eliminates methyl groups from lysine residues. KDM5A, also known as JARID1A or RBP2, belongs to the KDM5 Jumonji histone demethylase subfamily. To identify novel molecules that interact with the LSD5A receptor, we created a quantitative structure-activity relationship (QSAR) model. A group of 435 compounds was used in a study of the quantitative relationship between structure and activity to guess the IC50 values for blocking LASD5A. We used a genetic algorithm-multilinear regression-based quantitative structure-activity connection model to forecast the bioactivity (PIC50) of 1615 food and drug administration pharmaceuticals from the zinc database with the goal of repurposing clinically used medications. We used molecular docking, molecular dynamic simulation modelling, and molecular mechanics generalised surface area analysis to investigate the molecule's binding mechanism. A genetic algorithm and multi-linear regression method were used to make six variable-based quantitative structure-activity relationship models that worked well (R2 = 0.8521, Q2LOO = 0.8438, and Q2LMO = 0.8414). ZINC000000538621 was found to be a new hit against LSD5A after a quantitative structure-activity relationship-based virtual screening of 1615 zinc food and drug administration compounds. The docking analysis revealed that the hit molecule 11 in the KDM5A binding pocket adopted a conformation similar to the pdb-6bh1 ligand (docking score: -8.61 kcal/mol). The results from molecular docking and the quantitative structure-activity relationship were complementary and consistent. The most active lead molecule 11, which has shown encouraging results, has good absorption, distribution, metabolism, and excretion (ADME) properties, and its toxicity has been shown to be minimal. In addition, the MTT assay of ZINC000000538621 with MCF-7 cell lines backs up the in silico studies. We used molecular mechanics generalise borne surface area analysis and a 200-ns molecular dynamics simulation to find structural motifs for KDM5A enzyme interactions. Thus, our strategy will likely expand food and drug administration molecule repurposing research to find better anticancer drugs and therapies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rahul D Jawarkar
- Department of Medicinal Chemistry and Drug discovery, Dr. Rajendra Gode Institute of Pharmacy, Amravati, Maharashtra, India
| | - Magdi E A Zaki
- Department of Chemistry, Faculty of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Sami A Al-Hussain
- Department of Chemistry, Faculty of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Aamal A Al-Mutairi
- Department of Chemistry, Faculty of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Abdul Samad
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tishk International University, Erbil, Kurdistan Region, Iraq
| | - Vijay Masand
- Department of Chemistry, Amravati, Maharashtra, India
| | - Vivek Humane
- Department of Chemistry, Shri R. R. Lahoti Science college, Morshi District: Amravati, Maharashtra, India
| | - Suraj Mali
- School of Pharmacy, D.Y. Patil University (Deemed to be University), Nerul, Navi Mumbai, India
| | | | - Summya Rashid
- Department of Pharmacology & Toxicology, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Gehan M Elossaily
- Department of Basic Medical Sciences, College of Medicine, AlMaarefa University, Riyadh, Saudi Arabia
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Barazorda-Ccahuana HL, Cárcamo-Rodriguez EG, Centeno-Lopez AE, Galdino AS, Machado-de-Ávila RA, Giunchetti RC, Coelho EAF, Chávez-Fumagalli MA. Targeting with Structural Analogs of Natural Products the Purine Salvage Pathway in Leishmania (Leishmania) infantum by Computer-Aided Drug-Design Approaches. Trop Med Infect Dis 2024; 9:41. [PMID: 38393130 PMCID: PMC10891554 DOI: 10.3390/tropicalmed9020041] [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: 11/30/2023] [Revised: 01/27/2024] [Accepted: 01/29/2024] [Indexed: 02/25/2024] Open
Abstract
Visceral Leishmaniasis (VL) has a high death rate, with 500,000 new cases and 50,000 deaths occurring annually. Despite the development of novel strategies and technologies, there is no adequate treatment for the disease. Therefore, the purpose of this study is to find structural analogs of natural products as potential novel drugs to treat VL. We selected structural analogs from natural products that have shown antileishmanial activities, and that may impede the purine salvage pathway using computer-aided drug-design (CADD) approaches. For these, we started with the vastly studied target in the pathway, the adenine phosphoribosyl transferase (APRT) protein, which alone is non-essential for the survival of the parasite. Keeping this in mind, we search for a substance that can bind to multiple targets throughout the pathway. Computational techniques were used to study the purine salvage pathway from Leishmania infantum, and molecular dynamic simulations were used to gather information on the interactions between ligands and proteins. Because of its low homology to human proteins and its essential role in the purine salvage pathway proteins network interaction, the findings further highlight the significance of adenylosuccinate lyase protein (ADL) as a therapeutic target. An analog of the alkaloid Skimmianine, N,N-diethyl-4-methoxy-1-benzofuran-6-carboxamide, demonstrated a good binding affinity to APRT and ADL targets, no expected toxicity, and potential for oral route administration. This study indicates that the compound may have antileishmanial activity, which was granted in vitro and in vivo experiments to settle this finding in the future.
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Affiliation(s)
- Haruna Luz Barazorda-Ccahuana
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa María, Arequipa 04000, Peru
| | - Eymi Gladys Cárcamo-Rodriguez
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa María, Arequipa 04000, Peru
- Facultad de Ciencias Farmacéuticas, Bioquímicas y Biotecnológicas, Universidad Católica de Santa María, Arequipa 04000, Peru
| | - Angela Emperatriz Centeno-Lopez
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa María, Arequipa 04000, Peru
- Facultad de Ciencias Farmacéuticas, Bioquímicas y Biotecnológicas, Universidad Católica de Santa María, Arequipa 04000, Peru
| | - Alexsandro Sobreira Galdino
- Laboratório de Biotecnologia de Microrganismos, Universidade Federal São João Del-Rei, Divinópolis 35501-296, MG, Brazil
| | | | - Rodolfo Cordeiro Giunchetti
- Laboratório de Biologia das Interações Celulares, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil
- Instituto Nacional de Ciência e Tecnologia em Doenças Tropicais, INCT-DT, Salvador 40015-970, BA, Brazil
| | - Eduardo Antonio Ferraz Coelho
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil
- Departamento de Patologia Clínica, COLTEC, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil
| | - Miguel Angel Chávez-Fumagalli
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa María, Arequipa 04000, Peru
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Quraishi S, Saha D, Kumari K, Jha AN, Roy AS. Non-covalent binding interaction of bioactive coumarin esculetin with calf thymus DNA and yeast transfer RNA: A detailed investigation to decipher the binding affinities, binding location, interacting forces and structural alterations at a molecular level. Int J Biol Macromol 2024; 257:128568. [PMID: 38061533 DOI: 10.1016/j.ijbiomac.2023.128568] [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: 11/07/2023] [Revised: 11/28/2023] [Accepted: 11/30/2023] [Indexed: 01/26/2024]
Abstract
Esculetin is a well-known coumarin derivative found abundantly in nature possessing an extensive array of pharmacological and therapeutic properties. Consequently, to comprehend its molecular recognition mechanism, our objective is to conduct a complete investigation of its interactions with the nucleic acid, specifically ct-DNA, and t-RNA, using spectroscopic and computational techniques. The intrinsic fluorescence of esculetin is quenched when it interacts with ct-DNA and t-RNA, and this occurs through a static quenching mechanism. The thermodynamic parameters demonstrated that the interaction is influenced by hydrogen bonding and weak van der Waals forces. CD and FT-IR results revealed no conformational changes in ct-DNA and t-RNA structure on binding with esculetin. Furthermore, competitive displacement assay with ethidium bromide, melting temperature, viscosity measurement, and potassium iodide quenching experiments, reflected that esculetin probably binds to the minor groove of ct-DNA. The molecular docking results provided further confirmation for the spectroscopic findings, including the binding location of esculetin and binding energies of esculetin complexes with ct-DNA and t-RNA. Molecular dynamics simulation studies demonstrated the conformational stability and flexibility of nucleic acids.
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Affiliation(s)
- Sana Quraishi
- Department of Chemistry, National Institute of Technology Meghalaya, Shillong 793003, India
| | - Debanjan Saha
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur 784028, India
| | - Kalpana Kumari
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, India
| | - Anupam Nath Jha
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur 784028, India.
| | - Atanu Singha Roy
- Department of Chemistry, National Institute of Technology Meghalaya, Shillong 793003, India.
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9
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Baruah K, Singh AK, Kumari K, Nongbri DL, Jha AN, Singha Roy A. Interactions of Turmeric- and Curcumin-Functionalized Gold Nanoparticles with Human Serum Albumin: Exploration of Protein Corona Formation, Binding, Thermodynamics, and Antifibrillation Studies. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:1381-1398. [PMID: 38159065 DOI: 10.1021/acs.langmuir.3c03032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
In order to better understand the bioavailability and biocompatibility of polyphenol-assisted surface-modified bioengineered nanoparticles in nanomedicine applications, here, we address a series of photophysical experiments to quantify the binding affinity of serum albumin toward polyphenol-capped gold nanoparticles. For this, two different gold nanoparticles (AuNPs) were synthesized via the green synthesis approach, where curcumin and turmeric extract act as reducing as well as capping agents. The size, surface charge, and surface plasmon bands of the AuNPs were highly affected by the adsorption of human serum albumin (HSA) during protein corona formation, which was investigated using dynamic light scattering (DLS), ξ-potential, ultraviolet-visible (UV-vis) spectroscopy, and transmission electron microscopy (TEM) measurements. Fluorescence-based methods, absorbance, and SERS experiments were carried out to evaluate the binding aspects of AuNPs with HSA. We found that the AuNPs show moderate binding affinity toward HSA (Kb ∼ 104 M-1), irrespective of the capping agents on the surface. Hydrophobic association, along with some contribution of electrostatic interaction, played a key role in the binding process. The binding interaction was more toward the subdomain IIA region of HSA, as indicated by the competitive displacement studies using site-specific binders (warfarin and flufenamic acid). Because of the large surface curvature of small-sized AuNPs, the secondary structural conformations of HSA were slightly altered, as revealed by circular dichroism (CD), Fourier transform infrared (FT-IR) spectroscopy, and surface-enhanced Raman scattering (SERS) measurements. Additionally, the findings of the binding interactions were re-evaluated using molecular dynamics (MD) simulation studies by determining the root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), radius of gyration (Rg), and changes in the binding energy of HSA upon complexation with AuNPs. To determine the tentative evidence for pharmacokinetic administration, these biocompatible AuNPs were applied to inhibit the amyloid fibril formation of HSA and monitored by using the thioflavin T (ThT) assay, ANS fluorescence assay, fluorescence microscopic imaging, and FESEM. AuNPs were found to show better resistance toward fibrillation of the adsorbed protein.
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Affiliation(s)
- Kakali Baruah
- Department of Chemistry, National Institute of Technology Meghalaya, Shillong 793003, India
| | - Ajit Kumar Singh
- Department of Molecular Biology and Biotechnology, Tezpur University, Napaam, Tezpur 784028, Assam, India
| | - Kalpana Kumari
- Department of Bioscience and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam India
| | - Dasuk Lyngdoh Nongbri
- Department of Biotechnology & Bioinformatics, North-Eastern Hill University, Shillong 793022, India
| | - Anupam Nath Jha
- Department of Molecular Biology and Biotechnology, Tezpur University, Napaam, Tezpur 784028, Assam, India
| | - Atanu Singha Roy
- Department of Chemistry, National Institute of Technology Meghalaya, Shillong 793003, India
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Jha AN. Editorial: Computational approaches to build therapeutic paradigms targeting genes, proteins and pathways against neglected tropical diseases (NTDs). Front Genet 2023; 14:1183034. [PMID: 37265962 PMCID: PMC10230302 DOI: 10.3389/fgene.2023.1183034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 04/28/2023] [Indexed: 06/03/2023] Open
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Kumari P, Mamud A, Jha AN. Review on the Drug Intolerance and Vaccine Development for the Leishmaniasis. Curr Drug Targets 2023; 24:1023-1031. [PMID: 37823567 DOI: 10.2174/0113894501254585230927100440] [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: 03/23/2023] [Revised: 07/07/2023] [Accepted: 09/01/2023] [Indexed: 10/13/2023]
Abstract
Leishmaniasis is one of the Neglected Tropical Diseases (NTDs), a zoonotic disease of vector-borne nature that is caused by a protozoan parasite Leishmania. This parasite is transmitted by the vector sandfly into the human via a bite. Visceral leishmaniasis (VL), also called kala-azar, is the most fatal among the types of leishmaniasis, with high mortality mostly spread in the East Africa and South Asia regions. WHO report stated that approximately 3.3 million disabilities occur every year due to the disease along with approximately 50,000 annual deaths. The real matter of concern is that there is no particular effective medicine/vaccine available against leishmaniasis to date except a few approved drugs and chemotherapy for the infected patient. The current selection of small compounds was constrained, and their growing drug resistance had been a major worry. Additionally, the serious side effects on humans of the available therapy or drugs have made it essential to discover efficient and low-cost methods to speed up the development of new drugs against leishmaniasis. Ideally, the vaccine could be a low risk and effective alternative for both CL and VL and elicit long-lasting immunity against the disease. There are a number of vaccine candidates at various stages of clinical development and preclinical stage. However, none has successfully passed all clinical trials. But, the successful development and approval of commercially available vaccines for dogs against canine leishmaniasis (CanL) provides evidence that it can be possible for humans in distant future. In the present article, the approaches used for the development of vaccines for leishmaniasis are discussed and the progress being made is briefly reviewed.
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Affiliation(s)
- Priya Kumari
- Centre of Sustainable Polymers, Indian Institute of Technology, Guwahati, Assam, India
| | - Afrin Mamud
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, India
| | - Anupam Nath Jha
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, India
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