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Singh S, Kaushik AC, Gupta H, Jhinjharia D, Sahi S. Identification of Prognostic Markers and Potential Therapeutic Targets using Gene Expression Profiling and Simulation Studies in Pancreatic Cancer. Curr Comput Aided Drug Des 2024; 20:955-973. [PMID: 37711100 DOI: 10.2174/1573409920666230914100826] [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: 04/28/2023] [Revised: 07/07/2023] [Accepted: 08/08/2023] [Indexed: 09/16/2023]
Abstract
BACKGROUND Pancreatic ductal adenocarcinoma (PDAC) has a 5-year relative survival rate of less than 10% making it one of the most fatal cancers. A lack of early measures of prognosis, challenges in molecular targeted therapy, ineffective adjuvant chemotherapy, and strong resistance to chemotherapy cumulatively make pancreatic cancer challenging to manage. OBJECTIVE The present study aims to enhance understanding of the disease mechanism and its progression by identifying prognostic biomarkers, potential drug targets, and candidate drugs that can be used for therapy in pancreatic cancer. METHODS Gene expression profiles from the GEO database were analyzed to identify reliable prognostic markers and potential drug targets. The disease's molecular mechanism and biological pathways were studied by investigating gene ontologies, KEGG pathways, and survival analysis to understand the strong prognostic power of key DEGs. FDA-approved anti-cancer drugs were screened through cell line databases, and docking studies were performed to identify drugs with high affinity for ARNTL2 and PIK3C2A. Molecular dynamic simulations of drug targets ARNTL2 and PIK3C2A in their native state and complex with nilotinib were carried out for 100 ns to validate their therapeutic potential in PDAC. RESULTS Differentially expressed genes that are crucial regulators, including SUN1, PSMG3, PIK3C2A, SCRN1, and TRIAP1, were identified. Nilotinib as a candidate drug was screened using sensitivity analysis on CCLE and GDSC pancreatic cancer cell lines. Molecular dynamics simulations revealed the underlying mechanism of the binding of nilotinib with ARNTL2 and PIK3C2A and the dynamic perturbations. It validated nilotinib as a promising drug for pancreatic cancer. CONCLUSION This study accounts for prognostic markers, drug targets, and repurposed anti-cancer drugs to highlight their usefulness for translational research on developing novel therapies. Our results revealed potential and prospective clinical applications in drug targets ARNTL2, EGFR, and PI3KC2A for pancreatic cancer therapy.
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Affiliation(s)
- Samvedna Singh
- School of Biotechnology, Gautam Buddha University, Greater Noida, India
| | | | - Himanshi Gupta
- School of Biotechnology, Gautam Buddha University, Greater Noida, India
| | - Divya Jhinjharia
- School of Biotechnology, Gautam Buddha University, Greater Noida, India
| | - Shakti Sahi
- School of Biotechnology, Gautam Buddha University, Greater Noida, India
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Antony A, Veerappapillai S, Karuppasamy R. In-silico bioprospecting of secondary metabolites from endophytic Streptomyces spp. against Magnaporthe oryzae, a cereal killer fungus. 3 Biotech 2024; 14:15. [PMID: 38125652 PMCID: PMC10728396 DOI: 10.1007/s13205-023-03859-7] [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: 09/08/2023] [Accepted: 11/18/2023] [Indexed: 12/23/2023] Open
Abstract
Rice blast disease, caused by Magnaporthe oryzae, is the most devastating cereal killer worldwide. Note that melanin pigment is an essential factor of M. oryzae virulence, thus fungicides interfering with melanin biosynthesizing enzymes would reduce the pathogenicity. Scytalone dehydratase (SDH) is the key target for commercial fungicides, like carpropamid, due to its role in the dehydration reaction of the fungal melanin pathway. However, a single-point mutation (V75M) in SDH elicits resistance to carpropamid. A lack of effective fungicides against this resistant strain expedited the quest for novel bioactive inhibitors. Currently, bacterial endophytes like Streptomyces have been heralded for synthesizing bioactive metabolites to protect plants from phytopathogens. The literature search led to the identification of 21 Streptomyces spp. symbionts of paddy that can suppress M. oryzae growth. An antiSMASH server was used to explore Streptomyces spp. gene clusters and found 4463 putative metabolites. Besides, 745 unique metabolites were subjected to a series of virtual screening techniques. Ideally, this process identified five potential SDH inhibitors. The docking result highlights that the metabolite pseudopyronine A interacted hydrophobically with both Val75 of SDHWT and Met75 of SDHV75M targets. Moreover, pseudopyronine A has a higher binding free energy with SDHWT (- 89.94 kcal/mol) and SDHV75M (- 71.95 kcal/mol). Interestingly, the pyranones scaffold of pseudopyronine A was reported for antifungal activity against phytopathogens. Dynamic behavior confirms that pseudopyronine A has excellent conformational states with both SDHWT and SDHV75M. Altogether, we hope that this study creates a new avenue for the discovery of novel phytopathogen inhibitors from endophytes. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03859-7.
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Affiliation(s)
- Ajitha Antony
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014 India
| | - Shanthi Veerappapillai
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014 India
| | - Ramanathan Karuppasamy
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014 India
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Abida Ejaz S, Sajjad Bilal M, Aziz M, Wani TA, Zargar S, Fayyaz A, Hassan S, Ahmed A, Al Kahtani HM, Siddique F. Computational Exploration of Fluorocyclopentenyl-purines and-pyrimidines Derivatives as Potential Inhibitors of Epidermal Growth Factor Receptor (EGFR) for the Treatment of Breast Cancer. Chem Biodivers 2023; 20:e202301190. [PMID: 37963090 DOI: 10.1002/cbdv.202301190] [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: 08/09/2023] [Revised: 11/07/2023] [Accepted: 11/12/2023] [Indexed: 11/16/2023]
Abstract
The Epidermal Growth Factor Receptor (EGFR) is an important therapeutic target for the treatment of a variety of epithelial malignancies, including breast cancer, in which EGFR is aberrantly expressed.The fluorocyclopentenyl-purine-pyrimidines derivatives, which have previously been described as powerful compounds against breast cancer, were selected to investigate their potential against EGFR using computational tools in an effort to obtain potent inhibitors with fewer adverse effects. The molecule's chemical reactivity and stability were assessed by determining the HOMO-LUMO energy gap using density functional theory (DFT) calculations. Among all the selected compounds, PU4 displayed a HOMO-LUMO gap of 0.191 eV. Additionally, molecular docking analysis was performed to assess the binding affinities of PU4 within the active pocket of EGFR-TK. The compound PU4 showed potent interactions with EGFR exhibiting -32.3 kJ/mol binding energy which was found best as compared to gefitinib i. e., -27.4 kJ/mol which was further validated by molecular dynamics simulations and ADMET analysis. The results of these analyses indicate that the top hits obtained from the virtual screening possess the ability to act as effective EGFR inhibitor. Therefore, it is recommended to further investigate the inhibitory potential of these identified compounds using in vitro and in vivo approaches.
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Affiliation(s)
- Syeda Abida Ejaz
- Department of Pharmaceutical Chemistry, Faculty of Pharmacv, The Islamia University of, Bahawalpur, 63100, Pakistan
| | - Muhammad Sajjad Bilal
- Department of Pharmaceutical Chemistry, Faculty of Pharmacv, The Islamia University of, Bahawalpur, 63100, Pakistan
| | - Mubashir Aziz
- Department of Pharmaceutical Chemistry, Faculty of Pharmacv, The Islamia University of, Bahawalpur, 63100, Pakistan
| | - Tanveer A Wani
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh, 11451, Saudi Arabia
| | - Seema Zargar
- Department of Biochemistry, College of Science, King Saud University, P.O. Box, 22452, Riyadh 11451, Saudi Arabia
| | - Ammara Fayyaz
- Department of Pharmaceutical Chemistry, Faculty of Pharmacv, The Islamia University of, Bahawalpur, 63100, Pakistan
| | - Sidra Hassan
- Bahawalpur College of Pharmacy, Bahawalpur Medical and Dental College, Bahawalpur, Pakistan
| | - Aftab Ahmed
- Department of Pharmaceutical Chemistry, Faculty of Pharmacv, The Islamia University of, Bahawalpur, 63100, Pakistan
| | - Hammad M Al Kahtani
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh, 11451, Saudi Arabia
| | - Farhan Siddique
- Department of Pharmacy, Royal Institute of Medical Sciences (RIMS) Multan 60000, Pakistan
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409-1061, USA
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Tewari D, Rawat K, Bisht A, Almoyad MAA, Wahab S, Chandra S, Pande V. Screening of potential inhibitors of Leishmania major N-myristoyltransferase from Azadirachta indica phytochemicals for leishmaniasis drug discovery by molecular docking, molecular dynamics simulation and density functional theory methods. J Biomol Struct Dyn 2023:1-18. [PMID: 37922151 DOI: 10.1080/07391102.2023.2279281] [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: 07/24/2023] [Accepted: 10/30/2023] [Indexed: 11/05/2023]
Abstract
Leishmaniasis is one of the most neglected parasitic diseases worldwide. The toxicity of current drugs used for its treatment is a major obstacle to their effectiveness, necessitating the discovery and development of new therapeutic agents for better disease control. In Leishmania parasites, N-Myristoyltransferase (NMT) has been identified as a promising target for drug development. Thus, exploring well-known medicinal plants such as Azadirachta indica and their phytochemicals can offer a diverse range of treatment options, potentially leading to disease prevention and control. To assess the therapeutic potential of these compounds, their ADMET prediction and drug-likeness properties were analyzed. The top 4 compounds were selected which had better and significantly low binding energy than the reference molecule QMI. Based on the binding energy score of the top compounds, the results show that Isonimocinolide has the highest binding affinity (-9.8 kcal/mol). In addition, a 100 ns MD simulation of the four best compounds showed that Isonimocinolide and Nimbolide have good stability with LmNMT. These compounds were then subjected to MMPBSA (last 30 ns) calculation to analyze protein-ligand stability and dynamic behavior. Nimbolide and Meldenin showed lowest binding free energy i.e. -84.301 kJ/mol and -91.937 kJ/mol respectively. DFT was employed to calculate the HOMO-LUMO energy gap, global reactivity parameters, and molecular electrostatic potential of all hit molecules. The promising results obtained from MD simulations and MMPBSA analyses provide compelling evidence for the potential use of these compounds in future drug development efforts for the treatment of leishmaniasis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Disha Tewari
- Department of Biotechnology, Kumaun University, Bhimtal, Uttarakhand, India
| | - Kalpana Rawat
- Computational Biology & Biotechnology Laboratory, Department of Botany, Soban Singh Jeena University, Almora, Uttarakhand, India
| | - Amisha Bisht
- Department of Botany, P.G. College Bageshwar, Soban Singh Jeena University, Almora, Uttarakhand, India
| | - Mohammad Ali Abdullah Almoyad
- Department of Basic Medical Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Khamis Mushyt, Saudi Arabia
| | - Shadma Wahab
- Department of Pharmacognosy, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Subhash Chandra
- Computational Biology & Biotechnology Laboratory, Department of Botany, Soban Singh Jeena University, Almora, Uttarakhand, India
| | - Veena Pande
- Department of Biotechnology, Kumaun University, Bhimtal, Uttarakhand, India
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Fang Y, Liu F, Shi Y, Yang T, Xin Y, Gu Z, Shi G, Zhang L. N-terminal lid swapping contributes to the substrate specificity and activity of thermophilic lipase TrLipE. Front Microbiol 2023; 14:1193955. [PMID: 37434709 PMCID: PMC10332459 DOI: 10.3389/fmicb.2023.1193955] [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: 03/26/2023] [Accepted: 06/12/2023] [Indexed: 07/13/2023] Open
Abstract
TrLipE is a thermophilic lipase that has potential commercial applications because of its catalytic ability under extreme conditions. Consistent with most lipases, the lid of TrLipE is located over the catalytic pocket, controls the substrate channel to the active center, and regulates the substrate specificity, activity, and stability of the enzyme through conformational changes. TrLipE from Thermomicrobium roseum has potential industrial applications, which is hindered by its weak enzymatic activity. Here, 18 chimeras (TrL1-TrL18) were reconstructed by N-terminal lid swapping between TrLipE and structurally similar enzymes. The results showed that the chimeras had a similar pH range and optimum pH as wild TrLipE but a narrower temperature range of 40-80°C, and TrL17 and the other chimeras showed lower optimum temperatures of 70°C and 60°C, respectively. In addition, the half-lives of the chimeras were lower than those of TrLipE under optimum temperature conditions. Molecular dynamics simulations indicated that chimeras had high RMSD, RMSF, and B-factor values. When p-nitrophenol esters with different chains were used as substrates, compared with TrLipE, most of the chimeras had a low Km and high kcat value. The chimeras TrL2, TrL3, TrL17, and TrL18 could specifically catalyze the substrate 4-nitrophenyl benzoate, with TrL17 showing the highest kcat/Km value of 363.88 ± 15.83 L⋅min-1⋅mmol-1. Mutants were then designed by investigating the binding free energies of TrL17 and 4-nitrophenyl benzoate. The results indicated that single, double, and triple substitution variants (M89W and I206N; E33W/I206M and M89W/I206M; and M89W/I206M/L21I and M89W/I206N/L21I, respectively) presented approximately 2- to 3-fold faster catalysis of 4-nitrophenyl benzoate than the wild TrL17. Our observations will facilitate the development of the properties and industrial applications of TrLipE.
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Affiliation(s)
- Yakun Fang
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, Jiangsu, China
| | - Fan Liu
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, Jiangsu, China
| | - Yi Shi
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, Jiangsu, China
| | - Ting Yang
- Wuxi Food Safety Inspection and Test Center, Technology Innovation Center of Special Food for State Market Regulation, Wuxi, Jiangsu, China
| | - Yu Xin
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, Jiangsu, China
| | - Zhenghua Gu
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, Jiangsu, China
| | - Guiyang Shi
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, Jiangsu, China
| | - Liang Zhang
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, Jiangsu, China
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6
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Oyewusi HA, Akinyede KA, Abdul Wahab R, Huyop F. In silico analysis of a putative dehalogenase from the genome of halophilic bacterium Halomonas smyrnensis AAD6T. J Biomol Struct Dyn 2023; 41:319-335. [PMID: 34854349 DOI: 10.1080/07391102.2021.2006085] [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: 01/03/2023]
Abstract
Microbial-assisted removal of natural or synthetic pollutants is the prevailing green, low-cost technology to treat polluted environments. However, the challenge with enzyme-assisted bioremediation is the laborious nature of dehalogenase-producing microorganisms' bioprospecting. This bottleneck could be circumvented by in-silico analysis of certain microorganisms' whole-genome sequences to predict their protein functions and enzyme versatility for improved biotechnological applications. Herein, this study performed structural analysis on a dehalogenase (DehHsAAD6) from the genome of Halomonas smyrnensis AAD6 by molecular docking and molecular dynamic (MD) simulations. Other bioinformatics tools were also employed to identify substrate preference (haloacids and haloacetates) of the DehHsAAD6. The DehHsAAD6 preferentially degraded haloacids and haloacetates (-3.2-4.8 kcal/mol) and which formed three hydrogen bonds with Tyr12, Lys46, and Asp182. MD simulations data revealed the higher stability of DehHsAAD6-haloacid- (RMSD 0.22-0.3 nm) and DehHsAAD6-haloacetates (RMSF 0.05-0.14 nm) complexes, with the DehHsAAD6-L-2CP complex being the most stable. The detail of molecular docking calculations ranked complexes with the lowest binding free energies as: DehHsAAD6-L-2CP complex (-4.8 kcal/mol) = DehHsAAD6-MCA (-4.8 kcal/mol) < DehHsAAD6-TCA (-4.5 kcal/mol) < DehHsAAD6-2,3-DCP (-4.1 kcal/mol) < DehHsAAD6-D-2CP (-3.9 kcal/mol) < DehHsAAD6-2,2-DCP (-3.5 kcal/mol) < DehHsAAD6-3CP (-3.2 kcal/mol). In a nutshell, the study findings offer valuable perceptions into the elucidation of possible reaction mechanisms of dehalogenases for extended substrate specificity and higher catalytic activity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Habeebat Adekilekun Oyewusi
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia.,Enzyme Technology and Green Synthesis Research Group, Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia.,Department of Science Technology, Biochemistry unit, The Federal Polytechnic P.M.B, Ado Ekiti, Ekiti State, Nigeria
| | - Kolajo Adedamola Akinyede
- Department of Science Technology, Biochemistry unit, The Federal Polytechnic P.M.B, Ado Ekiti, Ekiti State, Nigeria.,Department of Medical Bioscience, University of the Western Cape, Bellville, Cape Town, South Africa
| | - Roswanira Abdul Wahab
- Enzyme Technology and Green Synthesis Research Group, Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia.,Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
| | - Fahrul Huyop
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia.,Enzyme Technology and Green Synthesis Research Group, Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
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Azimi SG, Bagherzade G, Saberi MR, Amiri Tehranizadeh Z. Discovery of New Ligand with Quinoline Scaffold as Potent Allosteric Inhibitor of HIV-1 and Its Copper Complexes as a Powerful Catalyst for the Synthesis of Chiral Benzimidazole Derivatives, and in Silico Anti-HIV-1 Studies. Bioinorg Chem Appl 2023; 2023:2881582. [PMID: 37125145 PMCID: PMC10147532 DOI: 10.1155/2023/2881582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 02/01/2023] [Accepted: 03/01/2023] [Indexed: 05/02/2023] Open
Abstract
In this paper, the novel Schiff base ligand containing quinoline moiety and its novel copper chelate complexes were successfully prepared. The catalytic activity of the final complex in the organic reaction such as synthesis of chiral benzimidazoles and anti-HIV-1 activity of Schiff base ligand and the products of this reaction were investigated. In addition, green chemistry reactions using microwaves, powerful catalyst synthesis, green recovery and reusability, and separation of products with economic, safe, and clean methods (green chemistry) are among the advantages of this protocol. The potency of these compounds as anti-HIV-1 agents was investigated using molecular docking into integrase (IN) enzyme with code 1QS4 and the GROMACS software for molecular dynamics simulation. The final steps were evaluated in case of RMSD, RMSF, and Rg. The results revealed that the compound VII exhibit a good binding affinity to integrase (Δg = -10.99 kcal/mol) during 100 ns simulation time, and the analysis of RMSD suggested that compound VII was stable in the binding site of integrase.
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Affiliation(s)
- Sabikeh G. Azimi
- Department of Chemistry, Faculty of Sciences, University of Birjand, Birjand 97175-615, Iran
| | - Ghodsieh Bagherzade
- Department of Chemistry, Faculty of Sciences, University of Birjand, Birjand 97175-615, Iran
| | - Mohammad Reza Saberi
- Department of Medical Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad 91775-1365, Iran
| | - Zeinab Amiri Tehranizadeh
- Department of Medical Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad 91775-1365, Iran
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FANANİ A, KURNİATİN PA, WAHYUDİ ST, NURCHOLİS W, AMBARSARİ L. Molecular Dynamics Simulation of E412 Catalytic Residue Mutation of GOx-IPBCC. JOURNAL OF THE TURKISH CHEMICAL SOCIETY, SECTION A: CHEMISTRY 2022. [DOI: 10.18596/jotcsa.1088587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
The enzyme glucose oxidase from Aspergillus niger has a homodimeric structure, consisting of two identical subunits with a molecular weight of 150,000 Daltons. In this study, we used the structure of the enzyme glucose oxidase from Aspergillus niger IPBCC.08.610 (GOx-IPBCC), this enzyme had a total activity of 92.87 U (μmol/min) and a Michaelis-Menten constant (Km) of 2.9 mM (millimolar). This study was conducted to predict the molecular dynamics of E412 (Glu412) residue catalytic mutation belonging to the GOx-IPBCC enzyme was determine the effect of changes in the catalytic residue on substrate binding (β-D-glucose). The results of molecular docking of 19 mutant structures, six E412 mutant homologous structures were selected (E412C, E412K, E412Q, E412T, E412, E412V, and E412W), which were evaluated using molecular dynamics simulation for 50 ns. The results showed a decrease in ∆G values in two mutant structures is E412C and E412T, and there is one mutant structure that increased ∆G values, namely E412W, these three mutant structures showed the best stability, bond interaction, and salt bridge profile according to molecular dynamics simulation.
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Dasmahapatra U, Kumar CK, Das S, Subramanian PT, Murali P, Isaac AE, Ramanathan K, MM B, Chanda K. In-silico molecular modelling, MM/GBSA binding free energy and molecular dynamics simulation study of novel pyrido fused imidazo[4,5-c]quinolines as potential anti-tumor agents. Front Chem 2022; 10:991369. [PMID: 36247684 PMCID: PMC9566731 DOI: 10.3389/fchem.2022.991369] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 08/29/2022] [Indexed: 11/21/2022] Open
Abstract
With an alarming increase in the number of cancer patients and a variety of tumors, it is high time for intensive investigation on more efficient and potent anti-tumor agents. Though numerous agents have enriched the literature, still there exist challenges, with the availability of different targets and possible cross-reactivity. Herein we have chosen the phosphoinositide 3-kinase (PI3K) as the target of interest and investigated the potential of pyrido fused imidazo[4,5-c]quinoline derivatives to bind strongly to the active site, thereby inhibiting the progression of various types of tumors. The AutoDock, Glide and the Prime-MM/GBSA analysis are used to execute the molecular docking investigation and validation for the designed compounds. The anti-tumor property evaluations were carried out by using PASS algorithm. Based on the GLIDE score, the binding affinity of the designed molecules towards the target PI3K was evaluated. The energetics associated with static interactions revealed 1j as the most potential candidate and the dynamic investigations including RMSD, RMSF, Rg, SASA and hydrogen bonding also supported the same through relative stabilization induced through ligand interactions. Subsequently, the binding free energy of the Wortmannin and 1j complex calculated using MM-PBSA analysis. Further evaluations with PASS prediction algorithm also supported the above results. The studies reveal that there is evidence for considering appropriate pyrido fused imidazo[4,5-c]quinoline compounds as potential anti-tumor agents.
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Affiliation(s)
- Upala Dasmahapatra
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Chitluri Kiran Kumar
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Soumyadip Das
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Prathima Thimma Subramanian
- Division of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Chennai campus, Chennai, Tamil Nadu, India
| | - Poornimaa Murali
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Arnold Emerson Isaac
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Karuppasamy Ramanathan
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Balamurali MM
- Division of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Chennai campus, Chennai, Tamil Nadu, India
- *Correspondence: Balamurali MM, ; Kaushik Chanda,
| | - Kaushik Chanda
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Vellore, Tamil Nadu, India
- *Correspondence: Balamurali MM, ; Kaushik Chanda,
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Samandar F, Tehranizadeh ZA, Saberi MR, Chamani J. CB1 as a novel target for Ginkgo biloba's terpene trilactone for controlling chemotherapy-induced peripheral neuropathy (CIPN). J Mol Model 2022; 28:283. [PMID: 36044079 DOI: 10.1007/s00894-022-05284-8] [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: 01/28/2022] [Accepted: 08/19/2022] [Indexed: 11/24/2022]
Abstract
The application of antineoplastic chemotherapeutic agents causes a common side effect known as chemotherapy-induced peripheral neuropathy (CIPN) that leads to reducing the quality of patient's life. This research involves the performance of molecular docking and molecular dynamic (MD) simulation studies to explore the impact of terpenoids of Ginkgo biloba on the targets (CB-1, TLR4, FAAH-1, COX-1, COX-2) that can significantly affect the controlling of CIPN's symptoms. According to the in-vitro and in-vivo investigations, terpenoids, particularly ginkgolides B, A, and bilobalide, can cause significant effects on neuropathic pain. The molecular docking results disclosed the tendency of our ligands to interact with mainly CB1 and FAAH-1, as well as partly with TLR4, throughout their interactions with targets. Terpene trilactone can exhibit a lower rate of binding energy than CB1's inhibitor (7dy), while being precisely located in the CB1's active site and capable of inducing stable interactions by forming hydrogen bonds. The analyses of MD simulation proved that ginkgolide B was a more suitable activator and inhibitor for CB1 and TLR4, respectively, when compared to bilobalide and ginkgolide A. Moreover, bilobalide is capable of inhibiting FAAH-1 more effectively than the two other ligands. According to the analyses of ADME, every three ligands followed the Lipinski's rule of five. Considering these facts, the exertion of three ligands is recommended for their anti-inflammatory, neuroprotective, and anti-nociception influences caused by primarily activating CB1 and inhibiting FAAH-1 and TLR4; in this regard, these compounds can stand as potential candidates for the control and treatment of CIPN's symptoms.
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Affiliation(s)
- Farzaneh Samandar
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Zeinab Amiri Tehranizadeh
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Mohammad Reza Saberi
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.,Bioinformatics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Jamshidkhan Chamani
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
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11
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Xiong L, Cao J, Yang X, Chen S, Wu M, Wang C, Xu H, Chen Y, Zhang R, Hu X, Chen T, Tang J, Deng Q, Li D, Yang Z, Xiao G, Zhang X. Exploring the mechanism of action of Xuanfei Baidu granule (XFBD) in the treatment of COVID-19 based on molecular docking and molecular dynamics. Front Cell Infect Microbiol 2022; 12:965273. [PMID: 36034710 PMCID: PMC9399524 DOI: 10.3389/fcimb.2022.965273] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 07/14/2022] [Indexed: 11/13/2022] Open
Abstract
PurposeThe Corona Virus Disease 2019 (COVID-19) pandemic has become a challenge of world. The latest research has proved that Xuanfei Baidu granule (XFBD) significantly improved patient’s clinical symptoms, the compound drug improves immunity by increasing the number of white blood cells and lymphocytes, and exerts anti-inflammatory effects. However, the analysis of the effective monomer components of XFBD and its mechanism of action in the treatment of COVID-19 is currently lacking. Therefore, this study used computer simulation to study the effective monomer components of XFBD and its therapeutic mechanism.MethodsWe screened out the key active ingredients in XFBD through TCMSP database. Besides GeneCards database was used to search disease gene targets and screen intersection gene targets. The intersection gene targets were analyzed by GO and KEGG. The disease-core gene target-drug network was analyzed and molecular docking was used for verification. Molecular dynamics simulation verification was carried out to combine the active ingredient and the target with a stable combination. The supercomputer platform was used to measure and analyze the number of hydrogen bonds, the binding free energy, the stability of protein target at the residue level, the solvent accessible surface area, and the radius of gyration.ResultsXFBD had 1308 gene targets, COVID-19 had 4600 gene targets, the intersection gene targets were 548. GO and KEGG analysis showed that XFBD played a vital role by the signaling pathways of immune response and inflammation. Molecular docking showed that I-SPD, Pachypodol and Vestitol in XFBD played a role in treating COVID-19 by acting on NLRP3, CSF2, and relieve the clinical symptoms of SARS-CoV-2 infection. Molecular dynamics was used to prove the binding stability of active ingredients and protein targets, CSF2/I-SPD combination has the strongest binding energy.ConclusionFor the first time, it was found that the important active chemical components in XFBD, such as I-SPD, Pachypodol and Vestitol, reduce inflammatory response and apoptosis by inhibiting the activation of NLRP3, and reduce the production of inflammatory factors and chemotaxis of inflammatory cells by inhibiting the activation of CSF2. Therefore, XFBD can effectively alleviate the clinical symptoms of COVID-19 through NLRP3 and CSF2.
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Affiliation(s)
- Li Xiong
- Clinical Medicine, Chengdu Medical College, Chengdu, China
| | - Junfeng Cao
- Clinical Medicine, Chengdu Medical College, Chengdu, China
| | - Xingyu Yang
- Clinical Medicine, Chengdu Medical College, Chengdu, China
| | - Shengyan Chen
- Clinical Medicine, Chengdu Medical College, Chengdu, China
| | - Mei Wu
- Clinical Medicine, Chengdu Medical College, Chengdu, China
| | - Chaochao Wang
- Clinical Medicine, Chengdu Medical College, Chengdu, China
| | - Hengxiang Xu
- Clinical Medicine, Chengdu Medical College, Chengdu, China
| | - Yijun Chen
- Clinical Medicine, Chengdu Medical College, Chengdu, China
| | - Ruijiao Zhang
- Chengdu Medical College of Basic Medical Sciences, Chengdu, China
| | - Xiaosong Hu
- Chengdu Medical College of Basic Medical Sciences, Chengdu, China
| | - Tian Chen
- Chengdu Medical College of Basic Medical Sciences, Chengdu, China
| | - Jing Tang
- Department of Infectious Diseases, First People’s Hospital of Ziyang, Ziyang, China
| | - Qin Deng
- Department of Infectious Diseases, First People’s Hospital of Ziyang, Ziyang, China
| | - Dong Li
- Clinical Medicine, Chengdu Medical College, Chengdu, China
| | - Zheng Yang
- Chengdu Medical College of Basic Medical Sciences, Chengdu, China
- *Correspondence: Xiao Zhang, ; Guibao Xiao, ; Zheng Yang,
| | - Guibao Xiao
- Department of Infectious Diseases, First People’s Hospital of Ziyang, Ziyang, China
- *Correspondence: Xiao Zhang, ; Guibao Xiao, ; Zheng Yang,
| | - Xiao Zhang
- Chengdu Medical College of Basic Medical Sciences, Chengdu, China
- *Correspondence: Xiao Zhang, ; Guibao Xiao, ; Zheng Yang,
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12
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Gao S, Zhang A, Ma D, Zhang K, Wang J, Wang X, Chen K. Enhancing pH stability of lysine decarboxylase via rational engineering and its application in cadaverine industrial production. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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13
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Lameh F, Baseer AQ, Ashiru AG. Comparative molecular docking and molecular-dynamic simulation of wild-type- and mutant carboxylesterase with BTA-hydrolase for enhanced binding to plastic. Eng Life Sci 2022; 22:13-29. [PMID: 35024024 PMCID: PMC8727734 DOI: 10.1002/elsc.202100083] [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: 07/10/2021] [Revised: 09/25/2021] [Accepted: 10/10/2021] [Indexed: 01/09/2023] Open
Abstract
According to the literature review, microbial degradation of polyethylene terephthalate by PETases has been detected effective and eco-friendly. However, the number of microorganisms capable of such feats is limited with some undesirable bioprospecting results. BTA-hydrolase has been already reported capable of degrading polyethylene terephthalate. Therefore, mutation by in silico site-directed mutagenesis means to introduce current isomer of PETase for polyethylene terephthalate degradative capability as a better approach to resolve this issue. This study aimed to use in silico site-directed mutagenesis to convert a carboxylesterase from Archaeoglobus fulgidus to BTA-hydrolase from Thermobifida fusca by replacing six amino acids in specific locations. This work was followed by molecular docking analysis with polyethylene terephthalate and polypropylene to compare their interactions. The best-docked enzyme-substrate complex was further subjected to molecular dynamics simulation to gauge the binding quality of the BTA-hydrolase, wild-type and mutant-carboxylesterase with only polyethylene terephthalate as a substrate. Results of molecular docking revealed lowest binding energy for the wild-type carboxylesterase-polypropylene complex (-7.5 kcal/mol). The root-mean-square deviation value was observed stable for BTA-hydrolase. Meanwhile, root-mean-square fluctuation was assessed with higher fluctuation for the mutated residue Lys178. Consequently, the Rg value for BTA-hydrolase-ligand complex (∼1.68 nm) was the lowest compared to the mutant and wild-type carboxylesterase. The collective data conveyed that mutations imparted a minimal change in the ability of the mutant carboxylesterase to bind to polyethylene terephthalate.
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Affiliation(s)
- Fatana Lameh
- Department of BotanyFaculty of BiologyKabul UniversityKabulAfghanistan
- Department of BiosciencesFaculty of ScienceUniversiti Teknologi MalaysiaJohor BahruMalaysia
| | - Abdul Qadeer Baseer
- Department of BiosciencesFaculty of ScienceUniversiti Teknologi MalaysiaJohor BahruMalaysia
- Department of BiologyFaculty of EducationKandahar UniversityKandaharAfghanistan
| | - Abubakar Garba Ashiru
- Department of ChemistryZamfara State College of EducationMaruNigeria
- Green Chemistry Research GroupDepartment of Chemistry, Faculty of ScienceUniversiti Teknologi MalaysiaJohor BahruMalaysia
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14
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Cai Y, Xing S, Zhang Q, Zhu R, Cheng K, Li C, Zeng X, He L. Expression, purification, properties, and substrate specificity analysis of Aspergillus niger GZUF36 lipase in Escherichia coli. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.09.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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15
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Pokhrel S, Bouback TA, Samad A, Nur SM, Alam R, Abdullah-Al-Mamun M, Nain Z, Imon RR, Talukder MEK, Tareq MMI, Hossen MS, Karpiński TM, Ahammad F, Qadri I, Rahman MS. Spike protein recognizer receptor ACE2 targeted identification of potential natural antiviral drug candidates against SARS-CoV-2. Int J Biol Macromol 2021; 191:1114-1125. [PMID: 34592225 PMCID: PMC8474879 DOI: 10.1016/j.ijbiomac.2021.09.146] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 09/14/2021] [Accepted: 09/21/2021] [Indexed: 01/19/2023]
Abstract
Angiotensin-converting enzyme 2 (ACE2), also known as peptidyl-dipeptidase A, belongs to the dipeptidyl carboxydipeptidases family has emerged as a potential antiviral drug target against SARS-CoV-2. Most of the ACE2 inhibitors discovered till now are chemical synthesis; suffer from many limitations related to stability and adverse side effects. However, natural, and selective ACE2 inhibitors that possess strong stability and low side effects can be replaced instead of those chemicals' inhibitors. To envisage structurally diverse natural entities as an ACE2 inhibitor with better efficacy, a 3D structure-based-pharmacophore model (SBPM) has been developed and validated by 20 known selective inhibitors with their correspondence 1166 decoy compounds. The validated SBPM has excellent goodness of hit score and good predictive ability, which has been appointed as a query model for further screening of 11,295 natural compounds. The resultant 23 hits compounds with pharmacophore fit score 75.31 to 78.81 were optimized using in-silico ADMET and molecular docking analysis. Four potential natural inhibitory molecules namely D-DOPA (Amb17613565), L-Saccharopine (Amb6600091), D-Phenylalanine (Amb3940754), and L-Mimosine (Amb21855906) have been selected based on their binding affinity (−7.5, −7.1, −7.1, and −7.0 kcal/mol), respectively. Moreover, 250 ns molecular dynamics (MD) simulations confirmed the structural stability of the ligands within the protein. Additionally, MM/GBSA approach also used to support the stability of molecules to the binding site of the protein that also confirm the stability of the selected four natural compounds. The virtual screening strategy used in this study demonstrated four natural compounds that can be utilized for designing a future class of potential natural ACE2 inhibitor that will block the spike (S) protein dependent entry of SARS-CoV-2 into the host cell.
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Affiliation(s)
- Sushil Pokhrel
- Department of Biomedical Engineering, State University of New York (SUNY), Binghamton, NY 13902, USA
| | - Thamer A Bouback
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Abdus Samad
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science, Jashore University of Science and Technology, Jashore 7408, Bangladesh; Laboratory of Computational Biology, Biological Solution Centre (BioSol Centre), Jashore 7408, Bangladesh
| | - Suza Mohammad Nur
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Rahat Alam
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science, Jashore University of Science and Technology, Jashore 7408, Bangladesh; Laboratory of Computational Biology, Biological Solution Centre (BioSol Centre), Jashore 7408, Bangladesh
| | - Md Abdullah-Al-Mamun
- Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna 9208, Bangladesh
| | - Zulkar Nain
- Laboratory of Computational Biology, Biological Solution Centre (BioSol Centre), Jashore 7408, Bangladesh; School of Medicine, University of Utah, Salt Lake City, UT 84112, USA
| | - Raihan Rahman Imon
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science, Jashore University of Science and Technology, Jashore 7408, Bangladesh; Laboratory of Computational Biology, Biological Solution Centre (BioSol Centre), Jashore 7408, Bangladesh
| | - Md Enamul Kabir Talukder
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science, Jashore University of Science and Technology, Jashore 7408, Bangladesh; Laboratory of Computational Biology, Biological Solution Centre (BioSol Centre), Jashore 7408, Bangladesh
| | - Md Mohaimenul Islam Tareq
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science, Jashore University of Science and Technology, Jashore 7408, Bangladesh; Laboratory of Computational Biology, Biological Solution Centre (BioSol Centre), Jashore 7408, Bangladesh
| | - Md Saddam Hossen
- Laboratory of Computational Biology, Biological Solution Centre (BioSol Centre), Jashore 7408, Bangladesh; Department of Biology, School of Life Science, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Tomasz M Karpiński
- Department of Medical Microbiology, Poznań University of Medical Sciences, Wieniawskiego 3, 61-712 Poznań, Poland
| | - Foysal Ahammad
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia; Laboratory of Computational Biology, Biological Solution Centre (BioSol Centre), Jashore 7408, Bangladesh.
| | - Ishtiaq Qadri
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
| | - Md Shahedur Rahman
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science, Jashore University of Science and Technology, Jashore 7408, Bangladesh.
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16
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Romes NB, Abdul Wahab R, Abdul Hamid M, Oyewusi HA, Huda N, Kobun R. Thermodynamic stability, in-vitro permeability, and in-silico molecular modeling of the optimal Elaeis guineensis leaves extract water-in-oil nanoemulsion. Sci Rep 2021; 11:20851. [PMID: 34675286 PMCID: PMC8531315 DOI: 10.1038/s41598-021-00409-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/17/2021] [Indexed: 11/09/2022] Open
Abstract
Nanoemulsion is a delivery system used to enhance bioavailability of plant-based compounds across the stratum corneum. Elaeis guineensis leaves are rich source of polyphenolic antioxidants, viz. gallic acid and catechin. The optimal E. guineensis leaves extract water-in-oil nanoemulsion was stable against coalescence, but it was under significant influence of Ostwald ripening over 90 days at 25 °C. The in-vitro permeability revealed a controlled and sustained release of the total phenolic compounds (TPC) of EgLE with a cumulative amount of 1935.0 ± 45.7 µgcm-2 after 8 h. The steady-state flux and permeation coefficient values were 241.9 ± 5.7 µgcm-2 h-1 and 1.15 ± 0.03 cm.h-1, respectively. The kinetic release mechanism for TPC of EgLE was best described by the Korsmeyer-Peppas model due to the highest linearity of R2 = 0.9961, indicating super case II transport mechanism. The in-silico molecular modelling predicted that the aquaporin-3 protein in the stratum corneum bonded preferably to catechin over gallic acid through hydrogen bonds due to the lowest binding energies of - 57.514 kcal/mol and - 8.553 kcal/mol, respectively. Thus, the in-silico study further verified that catechin could improve skin hydration. Therefore, the optimal nanoemulsion could be used topically as moisturizer to enhance skin hydration based on the in-silico prediction.
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Affiliation(s)
- Nissha Bharrathi Romes
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, 81310 UTM Johor, Bahru, Malaysia
- Enzyme Technology and Green Synthesis Group, Faculty of Science, Universiti Teknologi Malaysia, 81310 UTM Johor, Bahru, Malaysia
- School of Chemical and Energy Engineering, Faculty of Engineering, Universiti Teknologi Malaysia, 81310 UTM Johor, Bahru, Malaysia
| | - Roswanira Abdul Wahab
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, 81310 UTM Johor, Bahru, Malaysia.
- Enzyme Technology and Green Synthesis Group, Faculty of Science, Universiti Teknologi Malaysia, 81310 UTM Johor, Bahru, Malaysia.
| | - Mariani Abdul Hamid
- School of Chemical and Energy Engineering, Faculty of Engineering, Universiti Teknologi Malaysia, 81310 UTM Johor, Bahru, Malaysia
| | - Habeebat Adekilekun Oyewusi
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, 81310 UTM Johor, Bahru, Malaysia
- Enzyme Technology and Green Synthesis Group, Faculty of Science, Universiti Teknologi Malaysia, 81310 UTM Johor, Bahru, Malaysia
| | - Nurul Huda
- Faculty of Food Science and Nutrition, Universiti Malaysia Sabah, Kota Kinabalu, 88400, Sabah, Malaysia.
| | - Rovina Kobun
- Faculty of Food Science and Nutrition, Universiti Malaysia Sabah, Kota Kinabalu, 88400, Sabah, Malaysia
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Oyewusi HA, Huyop F, Wahab RA, Hamid AAA. In silico assessment of dehalogenase from Bacillus thuringiensis H2 in relation to its salinity-stability and pollutants degradation. J Biomol Struct Dyn 2021; 40:9332-9346. [PMID: 34014147 DOI: 10.1080/07391102.2021.1927846] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Increased scientific interest has led to the rise in biotechnological uses of halophilic and halotolerant microbes for hypersaline wastewater bioremediation. Hence, this study performed molecular docking, molecular dynamic (MD) simulations, and validation by Molecular Mechanic Poisson-Boltzmann Surface Area (MM-PBSA) calculations on the DehH2 from Bacillus thuringiensis H2. We aimed to identify the interactions of DehH2 with substrates haloacids, haloacetates, and chlorpyrifos under extreme salinity (35% NaCl). MD simulations revealed that DehH2 preferentially degraded haloacids and haloacetates (-6.3 to -4.7 kcal/mol) by forming three or four hydrogen bonds to the catalytic triad, Asp125, Arg201, and Lys202. Conversely, chlorpyrifos was the least preferred substrate in both MD simulations and MM-PBSA calculations. MD simulation results ranked the DehH2-L-2CP complex (RMSD □0.125-0.23 nm) as the most stable while the least was the DehH2-chlorpyrifos complex (RMSD 0.32 nm; RMSF 0.0 - 0.29). The order of stability was as follows: DehH2-L-2CP > DehH2-MCA > DehH2-D-2CP > DehH2-3CP > DehH2-2,2-DCP > DehH2-2,3-DCP > DehH2-TCA > DehH2-chlorpyrifos. The MM-PBSA calculations further affirmed the DehH2-L-2CP complex's highest stability with the lowest binding energy of -45.14 kcal/mol, followed closely by DehH2-MCA (-41.21 kcal/mol), DehH2-D-2CP (-31.59 kcal/mol), DehH2-3CP (-30.75 kcal/mol), DehH2-2,2- DCP (-29.72 kcal/mol), DehH2-2,3-DCP (-22.20 kcal/mol) and DehH2-TCA (-18.46 kcal/mol). The positive binding energy of the DehH2-chlorpyrifos complex (+180.57 kcal/mol) proved the enzyme's non-preference for the substrate. The results ultimately illustrated the unique specificity of the DehH2 to degrade the above-said pollutants under a hypersaline condition.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Habeebat Adekilekun Oyewusi
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Malaysia.,Enzyme Technology and Green Synthesis Research Group, Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Malaysia.,Department of Biochemistry, School of Science and Computer Studies, Federal Polytechnic Ado Ekiti, Ado Ekiti, Ekiti State, Nigeria
| | - Fahrul Huyop
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Malaysia.,Enzyme Technology and Green Synthesis Research Group, Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Malaysia
| | - Roswanira Abdul Wahab
- Enzyme Technology and Green Synthesis Research Group, Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Malaysia.,Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Malaysia
| | - Azzmer Azzar Abdul Hamid
- Department of Biotechnology, Kulliyyah of Science, International Islamic University Malaysia (IIUM), Kuantan Pahang, Malaysia
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18
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Oyewusi HA, Huyop F, Wahab RA. Molecular docking and molecular dynamics simulation of Bacillus thuringiensis dehalogenase against haloacids, haloacetates and chlorpyrifos. J Biomol Struct Dyn 2020; 40:1979-1994. [PMID: 33094694 DOI: 10.1080/07391102.2020.1835727] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The high dependency and surplus use of agrochemical products have liberated enormous quantities of toxic halogenated pollutants into the environment and threaten the well-being of humankind. Herein, this study performed molecular docking, molecular dynamic (MD) simulations, molecular mechanics-Poisson Boltzmann Surface Area (MM-PBSA) calculations on the DehH2 from Bacillus thuringiensis, to identify the order of which the enzyme degrades different substrates, haloacids, haloacetate and chlorpyrifos. The study discovered that the DehH2 favored the degradation of haloacids and haloacetates (-3.3 - 4.6 kcal/mol) and formed three hydrogen bonds with Asp125, Arg201 and Lys202. Despite the inconclusive molecular docking result, chlorpyrifos was consistently shown to be the least favored substrate of the DehH2 in MD simulations and MM-PBSA calculations. Results of MD simulations revealed the DehH2-haloacid- (RMSD 0.15 - 0.25 nm) and DehH2-haloacetates (RMSF 0.05 - 0.25 nm) were more stable, with the DehH2-L-2CP complex being the most stable while the least was the DehH2-chlorpyrifos (RMSD 0.295 nm; RMSF 0.05 - 0.59 nm). The Molecular Mechanics Poisson-Boltzmann Surface Area calculations showed the DehH2-L-2CP complex (-24.27 kcal/mol) having the lowest binding energy followed by DehH2-MCA (-22.78 kcal/mol), DehH2-D-2CP (-21.82 kcal/mol), DehH2-3CP (-21.11 kcal/mol), DehH2-2,2-DCP (-18.34 kcal/mol), DehH2-2,3-DCP (-8.34 kcal/mol), DehH2-TCA (-7.62 kcal/mol), while chlorpyrifos was unable to spontaneously bind to DehH2 (+127.16 kcal/mol). In a nutshell, the findings of this study offer valuable insights into the rational tailoring of the DehH2 for expanding its substrate specificity and catalytic activity in the near future.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Habeebat Adekilekun Oyewusi
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia.,Enzyme Technology and Green Synthesis Research Group, Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia.,Department of Biochemistry, School of Science and Computer Studies, Federal Polytechnic Ado Ekiti, Ado Ekiti PMB, Ekiti State, Nigeria
| | - Fahrul Huyop
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia.,Enzyme Technology and Green Synthesis Research Group, Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
| | - Roswanira Abdul Wahab
- Enzyme Technology and Green Synthesis Research Group, Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia.,Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
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19
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Elkarhat Z, Charoute H, Elkhattabi L, Barakat A, Rouba H. Potential inhibitors of SARS-cov-2 RNA dependent RNA polymerase protein: molecular docking, molecular dynamics simulations and MM-PBSA analyses. J Biomol Struct Dyn 2020; 40:361-374. [PMID: 32873176 DOI: 10.1080/07391102.2020.1813628] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The SARS-cov-2 RNA dependent RNA polymerase (nsp12) is a crucial viral enzyme that catalyzes the replication of RNA from RNA templates. The fixation of some ligands in the active site may alter the viral life cycle. The aim of the present study is to identify the conservation level of nsp12 motifs (A-G), using consurf server, and discover their interactions with rifabutin, rifampicin, rifapentin, sorangicin A, streptolydigin, myxopyronin B, VXR and VRX using AutoDockTools-1.5.6, Gromacs 2018.2 and g-mmpbsa. Thus, the most of amino acids residues located in nsp12 protein Motifs (A-G) were predicted as highly conserved. The binding energies of streptolydigin, VXR, rifabutin, rifapentine, VRX, sorangicin A, myxopyronin B and rifampicin with nsp12 protein are -8.11, -8.23, -7.14, -6.94, -6.55, -5.46, -5.33 and -5.26 kcal/mol, respectively. In the other hand, the binding energies of ligand in the same order with nsp7-nsp8-nsp12 complex are -7.23, -7.08, -7.21, -7, -6.59, -8.73, -5.52, -5.87 kcal/mol, respectively. All ligands interact with at least two nsp12 motifs. The molecular dynamics simulation of nsp12-streptolydigin and nsp12-VXR complexes shows that these two complexes are stable and the number of hydrogen bonds as a function of time, after 30 ns of simulation, varies between 0 and 6 for nsp12-streptolydigin complex and between 0 and 4 for nsp12-VXR complex. The average of free binding energies obtained using g_mmpbsa, after 30 ns of simulation, is -191.982 Kj/mol for nsp12-streptolydigin complex and -153.583 Kj/mol for nsp12-VXR complex. Our results suggest that these ligands may be used as inhibitors of SARS-cov-2 nsp12 protein.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Zouhair Elkarhat
- Laboratory of Genomics and Human Genetics, Département de la Recherche Scientifique, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Hicham Charoute
- Laboratory of Genomics and Human Genetics, Département de la Recherche Scientifique, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Lamiae Elkhattabi
- Laboratory of Genomics and Human Genetics, Département de la Recherche Scientifique, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Abdelhamid Barakat
- Laboratory of Genomics and Human Genetics, Département de la Recherche Scientifique, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Hassan Rouba
- Laboratory of Genomics and Human Genetics, Département de la Recherche Scientifique, Institut Pasteur du Maroc, Casablanca, Morocco
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