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Bukhari HA, Afzal M, Al-Abbasi FA, Sheikh RA, Alqurashi MM, Bawadood AS, Alzarea SI, Alamri A, Sayyed N, Kazmi I. In vivo and computational investigation of butin against alloxan-induced diabetes via biochemical, histopathological, and molecular interactions. Sci Rep 2024; 14:20633. [PMID: 39232184 PMCID: PMC11374895 DOI: 10.1038/s41598-024-71577-y] [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: 01/23/2024] [Accepted: 08/29/2024] [Indexed: 09/06/2024] Open
Abstract
Herbs have been used as medicines since antiquity, and it has been discovered that the human body responds well to herbal remedies. Research on the effect of butin was conducted in the current study in the alloxan-induced diabetic rat paradigm. A total of 30 Wistar rats were randomly assigned into the following groups (n = 6): I-Normal; II-Alloxan-induced (50 mg/kg); III-Alloxan + butin 25 mg/kg; IV-Alloxan + butin 50 mg/kg; V-Butin per se 50 mg/kg. Various diabetic parameters (blood glucose, insulin, HbA1c), lipid profile, inflammatory (TNF-α, IL-1β, IL-6 and NF-κB), antioxidant enzymes (CAT, SOD and GSH), oxidative stress indicators (MDA), apoptosis marker (caspase-3), hepatic markers (ALT and AST), and histopathological changes were assessed. Additionally, molecular docking and dynamics were performed to evaluate the interaction of butin with target proteins. Butin treatment, at both doses, significantly restored biochemical parameters and preserved pancreatic histopathology in diabetic rats. It effectively modulated blood parameters, lipid profiles, inflammatory markers, apoptosis, antioxidant enzyme activity, oxidative stress, and hepatic markers. Molecular docking revealed that butin binds to proteins such as caspase-3 (1NME), NF-κB (1SVC), and serum insulin (4IBM) with binding affinities of - 7.4, - 6.5, and - 8.2 kcal/mol, respectively. Molecular dynamics simulations further suggested that butin induces significant conformational changes in these proteins. Butin exhibits potential effects against alloxan-induced diabetic rats by restoring biochemical balance, reducing inflammation, and protecting pancreatic tissue. Its binding to key proteins involved in apoptosis and inflammation highlights its therapeutic potential in diabetes management.
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Affiliation(s)
- Hussam A Bukhari
- Department of Pathology, Faculty of Medicine, King Abdulaziz University, 21589, Jeddah, Saudi Arabia
- King Abdulaziz University Hospital, King Abdulaziz University, 21589, Jeddah, Saudi Arabia
| | - Muhammad Afzal
- Pharmacy Program, Department of Pharmaceutical Sciences, Batterjee Medical College, P.O. Box 6231, 21442, Jeddah, Saudi Arabia
| | - Fahad A Al-Abbasi
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, 21589, Jeddah, Saudi Arabia
| | - Ryan A Sheikh
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, 21589, Jeddah, Saudi Arabia
- Experimental Biochemistry Unit, King Fahd Medical Research Center, King Abdulaziz University, 21589, Jeddah, Saudi Arabia
| | - May M Alqurashi
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, 21589, Jeddah, Saudi Arabia
| | - Azizah Salim Bawadood
- Basic Medical Sciences Department, College of Medicine, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Sami I Alzarea
- Department of Pharmacology, College of Pharmacy, Jouf University, 72341, Aljouf, Sakaka, Saudi Arabia
| | - Abdulaziz Alamri
- Department of Biochemistry, College of Science, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Nadeem Sayyed
- School of Pharmacy, Glocal University, Saharanpur, 247121, India
| | - Imran Kazmi
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, 21589, Jeddah, Saudi Arabia.
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Dalbanjan NP, Praveen Kumar SK. A Chronicle Review of In-Silico Approaches for Discovering Novel Antimicrobial Agents to Combat Antimicrobial Resistance. Indian J Microbiol 2024; 64:879-893. [PMID: 39282180 PMCID: PMC11399514 DOI: 10.1007/s12088-024-01355-x] [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: 04/05/2024] [Accepted: 07/11/2024] [Indexed: 09/18/2024] Open
Abstract
Antimicrobial resistance (AMR) poses a foremost threat to global health, necessitating innovative strategies for discovering antimicrobial agents. This review explores the role and recent advances of in-silico techniques in identifying novel antimicrobial agents and combating AMR giving few briefings of recent case studies of AMR. In-silico techniques, such as homology modeling, virtual screening, molecular docking, pharmacophore modeling, molecular dynamics simulation, density functional theory, integrated machine learning, and artificial intelligence, are systematically reviewed for their utility in discovering antimicrobial agents. These computational methods enable the rapid screening of large compound libraries, prediction of drug-target interactions, and optimization of drug candidates. The review discusses integrating in-silico approaches with traditional experimental methods and highlights their potential to accelerate the discovery of new antimicrobial agents. Furthermore, it emphasizes the significance of interdisciplinary collaboration and data-sharing initiatives in advancing antimicrobial research. Through a comprehensive discussion of the latest developments in in-silico techniques, this review provides valuable insights into the future of antimicrobial research and the fight against AMR. Graphical Abstract Supplementary Information The online version contains supplementary material available at 10.1007/s12088-024-01355-x.
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Affiliation(s)
| | - S K Praveen Kumar
- Protein Biology Lab, Department of Biochemistry, Karnatak University, Dharwad, Karnataka 580003 India
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Khair-ul-Bariyah S, Sarfraz M, Arshad M, Waseem A, Khan HU, Khan S, Sharif A, Farooqi ZH, Ahmed E. Synthesis of 2-aminothiazole sulfonamides as potent biological agents: Synthesis, structural investigations and docking studies. Heliyon 2024; 10:e34980. [PMID: 39157352 PMCID: PMC11327602 DOI: 10.1016/j.heliyon.2024.e34980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 07/18/2024] [Accepted: 07/19/2024] [Indexed: 08/20/2024] Open
Abstract
A simplified synthetic approach involving sulfonylation followed by amino group alkylation produced new 2-aminothiazole derivatives. UV/Vis, infrared, and NMR spectroscopies confirmed their structures. Compounds 36, 22, 34, and 35 showed strong inhibition against Jack bean and Bacillus Pasteurii urease, with IC50 values from 14.06 to 20.21 μM/mL. Compounds 20, 26, 21, 29, 30, 31, and 32 exhibited potent inhibitory effects against α-glucosidase and α-amylase, with IC50 values between 20.34 and 37.20 μM/mL. Compounds 33, 26, and 27 demonstrated potent DPPH scavenging, with IC50 values around 34.4-39.2 μM/mL. FMO analysis showed compounds 21, 22, 24, and 25 having parallel aromatic ring systems due to π cloud interactions, while compounds 32 and 38 had distinct electronic density distributions. Compound 22 had HOMO and LUMO energy gaps of 5.805 eV, with bromo and fluoro substitutions in compounds 21 and 24 slightly increasing the gaps to 6.089 eV and 6.078 eV, respectively. Nitro groups in compounds 25 and 32 reduced the gaps to 0.384 eV and 1.187 eV. All compounds demonstrated high gastrointestinal absorption, non-permeability to the blood-brain barrier, and optimal skin permeation (Log Kp between -5.83 and -6.54 cm/s). Compounds 22, 24, and 38 had promising QED scores of 0.719, 0.707, and 0.860, respectively, with synthetic accessibility scores from 2.057 to 2.517. ADMET predictions indicated minimal toxicity, cardiovascular safety, and significant inhibitory potential for CYP enzymes. Strong in silico binding affinities (binding energies -5.75 to -7.63 kcal/mol) and metabolic stability suggest these derivatives are promising candidates for further drug development.
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Affiliation(s)
| | - Muhammad Sarfraz
- Institute of Chemistry, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | - Muhammad Arshad
- Institute of Chemistry, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | - Amir Waseem
- Department of Chemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Hidayat Ullah Khan
- Department of Chemistry, University of Science and Technology, Bannu, 28100, Pakistan
| | - Shahnaz Khan
- Department of Chemistry, University of Science and Technology, Bannu, 28100, Pakistan
| | - Ahsan Sharif
- School of Chemistry, University of the Punjab, 54590, Pakistan
| | | | - Ejaz Ahmed
- School of Chemistry, University of the Punjab, 54590, Pakistan
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Saikia Q, Adhikari K, Sanjeev A, Hazarika A, Sarma K. Isoliquiritigenin: a potential drug candidate for the management of erectile dysfunction. J Pharm Pharmacol 2024; 76:1065-1077. [PMID: 38865360 DOI: 10.1093/jpp/rgae054] [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: 10/06/2023] [Accepted: 04/23/2024] [Indexed: 06/14/2024]
Abstract
OBJECTIVE This study aimed to assess the erectogenic properties of isoliquiritigenin taking sildenafil (SDF) as the standard. METHODS The binding affinity of isoliquiritigenin (ISL) with the erectile marker proteins (endothelial nitric oxide synthase [eNOS] and enzyme phosphodiesterase type 5 [PDE5]) was investigated using Autodock Vina, which was validated using molecular dynamics simulation. Furthermore, the effect of ISL on the eNOS and PDE5 messenger ribonucleic acid (mRNA) expression and the sexual behavior of mice was investigated, along with the assessment of the pharmacokinetics of ISL. KEY FINDINGS The results revealed that the binding affinity of ISL-eNOS/PDE5 and SDF-eNOS/PDE5 was in the range of -7.5 to -8.6 kcal/mol. The ISL-eNOS/PDE5 complexes remained stable throughout the 100 ns simulation period. Root mean square deviation, Rg, SASA, hydrogen, and hydrophobic interactions were similar between ISL-eNOS/PDE5 and SDF-eNOS/PDE5. Analysis of mRNA expressions in paroxetine (PRX)-induced ED mice showed that the co-administration of PRX with ISL reduced PDE5 and increased eNOS mRNA expression, similar to the co-administered group (PRX+SDF). The sexual behavior study revealed that the results of PRX+ISL were better than those of the PRX+SDF group. Pharmacokinetic evaluation further demonstrated that ISL possesses drug-like properties. CONCLUSIONS The results showed that ISL is equally potent as SDF in terms of binding affinity, specific pharmacological properties, and modulating sexual behavior.
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Affiliation(s)
- Queen Saikia
- Department of Zoology, Mangaldai College, Mangaldai, Assam 784125, India
| | - Kamal Adhikari
- Department of Zoology, Tihu College, Tihu, Assam 781371, India
| | - Airy Sanjeev
- ACTREC, Sector 22, Utsav Chowk - CISF Rd, Owe Camp, Kharghar, Navi Mumbai, Maharashtra 410210, India
| | - Ajit Hazarika
- Tyagbir Hem Baruah College, Jamugurihat, Sonitpur, Assam 784189, India
| | - Kishore Sarma
- Department of Computational Biology and Biotechnology, Mahapurusha Srimanta Sankardeva Viswavidyalaya (Guwahati Unit), Rupnagar, Guwahati 781032, India
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Coelho GD, Silva MA, de Melo Pinheiro MA, Nadvorny D, Costa Amador V, Maia RT. In silico and in vitro assays suggests Congo red dye degradation by a Lentinus sp. laccase enzyme. J Biomol Struct Dyn 2024; 42:3802-3813. [PMID: 37254291 DOI: 10.1080/07391102.2023.2216282] [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: 01/23/2023] [Accepted: 05/12/2023] [Indexed: 06/01/2023]
Abstract
Laccase is a superfamily of ligninolytic enzymes known to degrade a wide variety of xenobiotics, including synthetic dyes. Congo Red (CR) has a diazo dye function, carcinogenic and mutagenic potential, and is currently applied in clinical analysis. The objective of this work was to produce and characterize the crude extract of Lentinus sp. in semi-solid fermentation (FSS) and perform in vitro and in silico studies to assess the potential of the crude extract to discolor the CR dye. Laccase activity was determined using ABTS as substrate and characterized. The in vitro discoloration was carried out using experimental design 22 at room temperature and monitored at 340 nm for 24h. Molecular docking and molecular dynamics simulations were performed between laccase and CR. The maximum laccase activity production was 29.63 U L-1 with six days of FSS. The optimal temperature and pH were 50 °C and 3.0, respectively. Discoloration of the CR dye was obtained only in tests containing CuSO4. Laccase formed stable complexes with the dye, presenting negative binding energy values ranging from -70.94 to -63.16 kcal mol-1 and the occurrence of seven hydrogen bonds. Molecular dynamics results showed the stability of the system (RMSD ranging from 1.0 to 2.5 Ä) and protein-ligand interaction along simulation. RMSF values pointed residues at the end of chains A (residues 300 to 305, 480 to 500) and B (residues 650 to 655 and 950 to 1000) as the most flexible regions of the laccase. This study highlighted the enzymatic action in the bioremediation of CR in vitro in agreement with the in silico simulations that demonstrate the enzyme potential.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Glauciane Danusa Coelho
- Center for Sustainable Development of the Semi-Arid, Academic Unit of Biotechnology Engineering, Federal University of Campina Grande, Sumé, Paraiba, Brazil
| | - Marco Antônio Silva
- Center for Water Resources and Environmental Studies, University of São Paulo, São Carlos School of Engineering, São Carlos, São Paulo, Brazil
| | - Maria Alice de Melo Pinheiro
- Post-Graduation in Materials Sciences, Center for Exact and Natural Sciences, Federal University of Pernambuco, Recife, Pernambuco, Brazil
| | - Daniela Nadvorny
- Department of Pharmaceutical Sciences, Federal University of Pernambuco, Recife, Pernambuco, Brazil
| | - Vinicius Costa Amador
- Post-Graduation in Biological Science, Federal University of Pernambuco, Recife, Pernambuco, Brazil
| | - Rafael Trindade Maia
- Center for Sustainable Development of the Semi-Arid, Academic Unit of Biotechnology Engineering, Federal University of Campina Grande, Sumé, Paraiba, Brazil
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Ghafoor D, Zeb A, Ali SS, Ali M, Akbar F, Ud Din Z, Ur Rehman S, Suleman M, Khan W. Immunoinformatic based designing of potential immunogenic novel mRNA and peptide-based prophylactic vaccines against H5N1 and H7N9 avian influenza viruses. J Biomol Struct Dyn 2024; 42:3641-3658. [PMID: 37222664 DOI: 10.1080/07391102.2023.2214228] [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: 10/31/2022] [Accepted: 05/10/2023] [Indexed: 05/25/2023]
Abstract
Influenza viruses are the most common cause of serious respiratory illnesses worldwide and are responsible for a significant number of annual fatalities. Therefore, it is crucial to look for new immunogenic sites that might trigger an effective immune response. In the present study, bioinformatics tools were used to design mRNA and multiepitope-based vaccines against H5N1 and H7N9 subtypes of avian influenza viruses. Several Immunoinformatic tools were employed to extrapolate T and B lymphocyte epitopes of HA and NA proteins of both subtypes. The molecular docking approach was used to dock the selected HTL and CTL epitopes with the corresponding MHC molecules. Eight (8) CTL, four (4) HTL, and Six (6) linear B cell epitopes were chosen for the structural arrangement of mRNA and of peptide-based prophylactic vaccine designs. Different physicochemical characteristics of the selected epitopes fitted with suitable linkers were analyzed. High antigenic, non-toxic, and non-allergenic features of the designed vaccines were noted at a neutral physiological pH. Codon optimization tool was used to check the GC content and CAI value of constructed MEVC-Flu vaccine, which were recorded to be 50.42% and 0.97 respectively. the GC content and CAI value verify the stable expression of vaccine in pET28a + vector. In-silico immunological simulation the MEVC-Flu vaccine construct revealed a high level of immune responses. The molecular dynamics simulation and docking results confirmed the stable interaction of TLR-8 and MEVC-Flu vaccine. Based on these parameters, vaccine constructs can be regarded as an optimistic choice against H5N1 and H7N9 strains of the influenza virus. Further experimental testing of these prophylactic vaccine designs against pathogenic avian influenza strains may clarify their safety and efficacy.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dawood Ghafoor
- Center for Biosafety Mega-Science, Chinese Academy of Sciences, CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Wuhan, Hubei, China
| | - Adnan Zeb
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Syed Shujait Ali
- Centre for Biotechnology and Microbiology, University of Swat, Swat, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Ali
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Fazal Akbar
- Centre for Biotechnology and Microbiology, University of Swat, Swat, Khyber Pakhtunkhwa, Pakistan
| | - Zia Ud Din
- Center for Advanced Studies in Vaccinology and Biotechnology, University of Balochistan Quetta, Quetta, Pakistan
| | - Shoaib Ur Rehman
- Department of Biotechnology, University of Science and Technology, Bannu, Pakistan
| | - Muhammad Suleman
- Centre for Biotechnology and Microbiology, University of Swat, Swat, Khyber Pakhtunkhwa, Pakistan
| | - Wajid Khan
- Centre for Biotechnology and Microbiology, University of Swat, Swat, Khyber Pakhtunkhwa, Pakistan
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Onisuru O, Achilonu I. Describing the ligandin properties of Plasmodium falciparum and vivax glutathione transferase towards bromosulfophthalein from empirical and computational modelling viewpoints. J Biomol Struct Dyn 2024:1-16. [PMID: 38506165 DOI: 10.1080/07391102.2024.2329291] [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: 12/14/2023] [Accepted: 03/06/2024] [Indexed: 03/21/2024]
Abstract
Research has spotlighted glutathione transferase (GST) as a promising target for antimalarial drug development due to its pivotal role in cellular processes, including metabolizing toxins and managing oxidative stress. This interest arises from GST's potential to combat multidrug resistance in existing antimalarial drugs. Plasmodium falciparum GST (PfGST) and Plasmodium vivax GST (PvGST) are key targets; inhibiting them not only disrupt detoxification but also reduce their antioxidant capacity, a critical feature for potent antimalarials. Bromosulfophthalein (BSP), a clinical liver function dye, emerged as a potent cytosolic GST inhibitor. This study explored BSP's inhibitory properties on PfGST and PvGST, showcasing its binding capabilities through empirical and computational analyses. The study revealed BSP's ability to significantly inhibit GST activity, altering the proteins' structures and stability. Specifically, BSP binding induced spectral changes and impacted the proteins' thermal stability, reducing their melting temperatures. Computational simulations highlighted BSP's strong binding to PfGST and PvGST at their dimer interface, stabilized by various interactions, including hydrogen bonds and van der Waals forces. Notably, BSP's binding altered the proteins' compactness and conformational dynamics, suggesting a potential non-competitive, allosteric inhibition mechanism. This study provided novel insights into BSP's candidacy as an antimalarial drug by targeting PfGST and PvGST. Its ability to disrupt crucial functions of these enzymes' positions BSP as a promising candidate for further drug development in combating malariaCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Olalekan Onisuru
- Protein Structure-Function and Research Unit, School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, Braamfontein, Johannesburg, South Africa
| | - Ikechukwu Achilonu
- Protein Structure-Function and Research Unit, School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, Braamfontein, Johannesburg, South Africa
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Mohd Radzuan SN, Phongphane L, Abu Bakar MH, Che Omar MT, Nor Shahril NS, Supratman U, Harneti D, Wahab HA, Azmi MN. Synthesis, biological activities, and evaluation molecular docking-dynamics studies of new phenylisoxazole quinoxalin-2-amine hybrids as potential α-amylase and α-glucosidase inhibitors. RSC Adv 2024; 14:7684-7698. [PMID: 38444963 PMCID: PMC10912921 DOI: 10.1039/d3ra08642a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 02/28/2024] [Indexed: 03/07/2024] Open
Abstract
New phenylisoxazole quinoxalin-2-amine hybrids 5a-i were successfully synthesised with yields of 53-85% and characterised with various spectroscopy methods. The synthesised hybrids underwent in vitro α-amylase and α-glucosidase inhibitory assays, with acarbose as the positive control. Through the biological study, compound 5h exhibits the highest α-amylase inhibitory activity with IC50 = 16.4 ± 0.1 μM while compounds 5a-c, 5e and 5h exhibit great potential as α-glucosidase inhibitors, with 5c being the most potent (IC50 = 15.2 ± 0.3 μM). Among the compounds, 5h exhibits potential as a dual inhibitor for both α-amylase (IC50 = 16.4 ± 0.1 μM) and α-glucosidase (IC50 = 31.6 ± 0.4 μM) enzymes. Through the molecular docking studies, the inhibition potential of the selected compounds is supported. Compound 5h showed important interactions with α-amylase enzyme active sites and exhibited the highest binding energy of -8.9 ± 0.10 kcal mol-1, while compound 5c exhibited the highest binding energy of -9.0 ± 0.20 kcal mol-1 by forming important interactions with the α-glucosidase enzyme active sites. The molecular dynamics study showed that the selected compounds exhibited relative stability when binding with α-amylase and α-glucosidase enzymes. Additionally, compound 5h demonstrated a similar pattern of motion and mechanism of action as the commercially available miglitol.
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Affiliation(s)
| | - Lacksany Phongphane
- School of Chemical Sciences, Universiti Sains Malaysia 11800 Minden Penang Malaysia
| | - Mohamad Hafizi Abu Bakar
- Bioprocess Technology Division, School of Industrial Technology, Universiti Sains Malaysia 11800 Minden Penang Malaysia
| | - Mohammad Tasyriq Che Omar
- Biological Section, School of Distance Education, Universiti Sains Malaysia 11800 Minden Penang Malaysia
| | - Nor Shafiqah Nor Shahril
- Bioprocess Technology Division, School of Industrial Technology, Universiti Sains Malaysia 11800 Minden Penang Malaysia
| | - Unang Supratman
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran 45363 Jatinangor Indonesia
| | - Desi Harneti
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran 45363 Jatinangor Indonesia
| | - Habibah A Wahab
- School of Pharmaceutical Sciences, Universiti Sains Malaysia 11800 Minden Penang Malaysia
| | - Mohamad Nurul Azmi
- School of Chemical Sciences, Universiti Sains Malaysia 11800 Minden Penang Malaysia
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Jia R, Yang Y, Liao G, Wu H, Yang C, Wang G. Flavor Characteristics of Umami Peptides from Wuding Chicken Revealed by Molecular Dynamics Simulation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:3673-3682. [PMID: 38290215 DOI: 10.1021/acs.jafc.3c08348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Wuding chicken is famous for its delicious meat, and HLEEEIK, LDDALR, and ELY were jointly extracted from different processing stages of Wuding chicken. However, whether these peptides can be used as umami supplements is unclear. The sensory evaluation tests were used to study the taste characteristics. The secondary structure of the peptides and their interaction with T1R1/T1R3 were predicted by the circular dichroism spectrum and molecular dynamics simulation. The umami threshold was 0.03125 to 0.06250 mg/mL, all of which could increase umami, saltiness, sweetness, and mask bitterness. Compared with HLEEEIK, the frequency of umami active fragments and the improvement rate of the umami score of EEE increased by 133.35% and 40.09%, respectively. Peptides were dominated by umami taste according to sensory analysis, among which EE-3 (3.18) has the highest umami intensity followed by LR-4 (2.58), HK-7 (2.13), and EY-3 (1.82). The main secondary structure of umami peptides was β-folding, and Tyr74, Arg323, Arg272, and Gln35 were the key amino acid residues for binding of umami peptides to the receptor. This study further elucidated that the umami intensity of the peptides could be altered by changing the sequence composition of the peptides, which enhanced our understanding of the complex flavor properties of umami peptides.
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Affiliation(s)
- Rong Jia
- College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, China
- Livestock Product Processing and Engineering Technology Research Center of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
| | - Yuan Yang
- College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, China
- Livestock Product Processing and Engineering Technology Research Center of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
| | - Guozhou Liao
- Livestock Product Processing and Engineering Technology Research Center of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
| | - Hongyan Wu
- College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, China
- Livestock Product Processing and Engineering Technology Research Center of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
| | - Chunfang Yang
- College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, China
- Livestock Product Processing and Engineering Technology Research Center of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
| | - Guiying Wang
- College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, China
- Livestock Product Processing and Engineering Technology Research Center of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
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Alshammari SO. Marine Brown Algae-Derived Compounds as Potential Inhibitors of Japanese Encephalitis Virus RNA-Dependent RNA Polymerase. Mar Drugs 2024; 22:92. [PMID: 38393063 PMCID: PMC10890675 DOI: 10.3390/md22020092] [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: 01/22/2024] [Revised: 02/07/2024] [Accepted: 02/12/2024] [Indexed: 02/25/2024] Open
Abstract
The Japanese encephalitis virus (JEV) is a mosquito-borne flavivirus that primarily affects people in Asia and seriously threatens public health. Considering the rising occurrence rates and lack of targeted antiviral treatments, it is essential to comprehend and tackle obstacles related to JEV in order to lessen its influence on world health. This investigation explores compounds derived from marine brown algae (Phaeophyceae) as potential inhibitors of JEV RNA-dependent RNA polymerase (RdRp), a critical enzyme in the virus's replication cycle. Employing the computational virtual screen approach, four compounds, i.e., CMNPD16749, CMNPD2606, CMNPD27817, and CMNPD23662, with favorable binding energies ranging from -15.7 Kcal/mol to -13.9 kcal/mol were identified. Subsequently, through molecular docking analysis, the interactions responsible for the binding stability between the target protein and hit molecules compared to the reference molecule Galidesvir were studied. Further, through extensive molecular dynamic (MD) simulation studies at 200 ns, it was confirmed that each docked complex showed acceptable dynamic stability compared to the reference molecule. These findings were further validated using MM/PBSA free binding energy calculations, PCA analysis and free energy landscape construction. These computational findings suggested that the brown algae-derived compounds may act as an antiviral drug against JEV infection and lay a crucial foundation for future experimental studies against JEV.
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Affiliation(s)
- Saud O Alshammari
- Department of Pharmacognosy and Alternative Medicine, Faculty of Pharmacy, Northern Border University, Rafha 76321, Saudi Arabia
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Gunasekaran V, Dhakshinamurthy SS. Computational Insights into the Interaction of Pinostrobin with Bcl-2 Family Proteins: A Molecular Docking Analysis. Asian Pac J Cancer Prev 2024; 25:507-512. [PMID: 38415536 PMCID: PMC11077126 DOI: 10.31557/apjcp.2024.25.2.507] [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: 08/12/2023] [Accepted: 02/18/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND Cancer research has emphasized the Bcl-2 family of proteins because of their interaction in apoptosis process, a critical mechanism that regulates cellular survival and death. Recently small molecules from diverse sources have gained much attention in anticancer research due to their promising inhibitory action against Bcl-2 and Bcl-XL that are pointedly known as the members of anti-apoptotic Bcl-2 family of proteins. Pinostrobin (PN) is a natural flavonoid with diverse pharmacological potential emerged as a molecule of interest as anticancer agent. The present study aims to screen the interaction of PN with anti-apoptotic protagonists Bcl-2 and Bcl- XL at the molecular level through docking studies. METHOD The molecular docking was performed using the Schrodinger software. The docking score of PN with the Bcl-2 (4IEH) and Bcl-XL (3ZK6) and their molecular interactions was examined and analysed. RESULTS The result of the molecular docking analysis showed that PN and the anti-apoptotic proteins 4IEH and 3ZK6 had significant interactions and docking energy scores (ΔG) were found to be -5.112 kcal/mol and -7.822 kcal/mol respectively. The small molecule PN illustrated effective interaction with the active site amino acids of the Bcl-2 and Bcl-XL proteins and has been associated through traditional hydrogen bond with 4IEH. Further, it was observed that PN and anti-apoptotic Bcl-2 proteins interaction was stabilized by other non-covalent interactions, such as π-alkyl or π-π interactions and van der Waals forces. CONCLUSIONS This was the first study to reveal the inhibitory action of PN against anti-apoptotic Bcl-2 and Bcl-XL proteins at the molecular level. The findings of this study concludes that PN ability to inhibit anti-apoptotic proteins, Bcl-2 and Bcl-XL could be useful to induce intracellular apoptosis in tumorous cells.
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Wahhab BH, Oyewusi HA, Wahab RA, Mohammad Hood MH, Abdul Hamid AA, Al-Nimer MS, Edbeib MF, Kaya Y, Huyop F. Comparative modeling and enzymatic affinity of novel haloacid dehalogenase from Bacillus megaterium strain BHS1 isolated from alkaline Blue Lake in Turkey. J Biomol Struct Dyn 2024; 42:1429-1442. [PMID: 37038649 DOI: 10.1080/07391102.2023.2199870] [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: 08/13/2022] [Accepted: 04/01/2023] [Indexed: 04/12/2023]
Abstract
This study presents the initial structural model of L-haloacid dehalogenase (DehLBHS1) from Bacillus megaterium BHS1, an alkalotolerant bacterium known for its ability to degrade halogenated environmental pollutants. The model provides insights into the structural features of DehLBHS1 and expands our understanding of the enzymatic mechanisms involved in the degradation of these hazardous pollutants. Key amino acid residues (Arg40, Phe59, Asn118, Asn176, and Trp178) in DehLBHS1 were identified to play critical roles in catalysis and molecular recognition of haloalkanoic acid, essential for efficient binding and transformation of haloalkanoic acid molecules. DehLBHS1 was modeled using I-TASSER, yielding a best TM-score of 0.986 and an RMSD of 0.53 Å. Validation of the model using PROCHECK revealed that 89.2% of the residues were located in the most favored region, providing confidence in its structural accuracy. Molecular docking simulations showed that the non-simulated DehLBHS1 preferred 2,2DCP over other substrates, forming one hydrogen bond with Arg40 and exhibiting a minimum energy of -2.5 kJ/mol. The simulated DehLBHS1 exhibited a minimum energy of -4.3 kJ/mol and formed four hydrogen bonds with Arg40, Asn176, Asp9, and Tyr11, further confirming the preference for 2,2DCP. Molecular dynamics simulations supported this preference, based on various metrics, including RMSD, RMSF, gyration, hydrogen bonding, and molecular distance. MM-PBSA calculations showed that the DehLBHS1-2,2-DCP complex had a markedly lower binding energy (-21.363 ± 1.26 kcal/mol) than the DehLBHS1-3CP complex (-14.327 ± 1.738 kcal/mol). This finding has important implications for the substrate specificity and catalytic function of DehLBHS1, particularly in the bioremediation of 2,2-DCP in contaminated alkaline environments. These results provide a detailed view of the molecular interactions between the enzyme and its substrate and may aid in the development of more efficient biocatalytic strategies for the degradation of halogenated compounds.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Batool Hazim Wahhab
- Department of Microbiology, Faculty of Medicine, Al-Mustansiriyah University, Iraq
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Malaysia
| | - Habeebat Adekilekun Oyewusi
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Malaysia
- Department of Biochemistry, School of Science and Computer Studies, Federal Polytechnic Ado Ekiti, Ekiti State, Nigeria
| | - Roswanira Abdul Wahab
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Malaysia
| | - Mohammad Hakim Mohammad Hood
- Department of Biotechnology, Kulliyah of Science, International Islamic University Malaysia, Kuantan, Pahang, Malaysia
| | - Azzmer Azzar Abdul Hamid
- Department of Biotechnology, Kulliyah of Science, International Islamic University Malaysia, Kuantan, Pahang, Malaysia
| | - Marwan Salih Al-Nimer
- Department of Pharmacology, College of Medicine, University of Diyala, Baqubah, Iraq
| | - Mohamed Faraj Edbeib
- Department of Medical Laboratories, Faculty of Medical Technology, Bani Walid University, Libya
| | - Yilmaz Kaya
- Department of Biology, Faculty of Science, Kyrgyz-Turkish Manas University, Bishkek, Kyrgyzstan
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayis University, Samsun, Turkey
| | - Fahrul Huyop
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Malaysia
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Rabaan AA, Almansour ZH, Al Bshabshe A, Halwani MA, Al-Subaie MF, Al Kaabi NA, Alshamrani SA, Alshehri AA, Nahari MH, Alqahtani AS, Alhajri M, Alissa M. Application of temperature-dependent and steered molecular dynamics simulation to screen anti-dengue compounds against Marburg virus. J Biomol Struct Dyn 2024:1-20. [PMID: 38234048 DOI: 10.1080/07391102.2024.2303386] [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: 06/20/2023] [Accepted: 01/03/2024] [Indexed: 01/19/2024]
Abstract
Marburg virus infections are extremely fatal with a fatality range of 23% to 90%, therefore there is an urgent requirement to design and develop efficient therapeutic molecules. Here, a comprehensive temperature-dependent molecular dynamics (MD) simulation method was implemented to identify the potential molecule from the anti-dengue compound library that can inhibit the function of the VP24 protein of Marburg. Virtual high throughput screening identified five effective binders of VP24 after screening 484 anti-dengue compounds. These compounds were treated in MD simulation at four different temperatures: 300, 340, 380, and 420 K. Higher temperatures showed dissociation of hit compounds from the protein. Further, triplicates of 100 ns MD simulation were conducted which showed that compounds ID = 118717693, and ID = 5361 showed strong stability with the protein molecule. These compounds were further validated using Δ G binding free energies and they showed: -30.38 kcal/mol, and -67.83 kcal/mol binding free energies, respectively. Later, these two compounds were used in steered MD simulation to detect its dissociation. Compound ID = 5361 showed the maximum pulling force of 199.02 kcal/mol/nm to dissociate the protein-ligand complex while ID = 118717693 had a pulling force of 101.11 kcal/mol/nm, respectively. This ligand highest number of hydrogen bonds with varying occupancies at 89.93%, 69.80%, 57.93%, 52.33%, and 50.63%. This study showed that ID = 5361 can bind with the VP24 strongly and has the potential to inhibit its function which can be validated in the in-vitro experiment.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
- Department of Public Health and Nutrition, The University of Haripur, Haripur, Pakistan
| | - Zainab H Almansour
- Biological Science Department, College of Science, King Faisal University, Hofuf, Saudi Arabia
| | - Ali Al Bshabshe
- Adult critical care Department of Medicine, Division of adult critical care, College of Medicine, King Khalid University, Abha, Saudi Arabia
| | - Muhammad A Halwani
- Department of Medical Microbiology, Faculty of Medicine, Al Baha University, Saudi Arabia
| | - Maha F Al-Subaie
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
- Research Center, Dr. Sulaiman Alhabib Medical Group, Riyadh, Saudi Arabia
| | - Nawal A Al Kaabi
- College of Medicine and Health Science, Khalifa University, Abu Dhabi, United Arab Emirates
- Sheikh Khalifa Medical City, Abu Dhabi Health Services Company (SEHA), Abu Dhabi, United Arab Emirates
| | - Saleh A Alshamrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran, Saudi Arabia
| | - Ahmad A Alshehri
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran, Saudi Arabia
| | - Mohammed H Nahari
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran, Saudi Arabia
| | - Ali S Alqahtani
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Mashael Alhajri
- Department of Internal Medicine, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Mohammed Alissa
- Department of Medical Laboratory, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj, Saudi Arabia
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Ganegamage S, Ramirez E, Alnakhala H, Tripathi A, Nguyen CCD, Zami A, Ostafe R, Tian S, Dettmer U, Fortin JS. 1,4-Diurea- and 1,4-Dithiourea-Substituted Aromatic Derivatives Selectively Inhibit α-Synuclein Oligomer Formation In Vitro. ACS OMEGA 2024; 9:1216-1229. [PMID: 38222653 PMCID: PMC10785335 DOI: 10.1021/acsomega.3c07453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/28/2023] [Accepted: 11/30/2023] [Indexed: 01/16/2024]
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disease, affecting the elderly population worldwide. In PD, the misfolding of α-synuclein (α-syn) results in the formation of inclusions referred to as Lewy bodies (LB) in midbrain neurons of the substantia nigra and other specific brain localizations, which is associated with neurodegeneration. There are no approved strategies to reduce the formation of LB in the neurons of patients with PD. Our drug discovery program focuses on the synthesis of urea and thiourea compounds coupled with aminoindole moieties to abrogate α-syn aggregation and to slow down the progression of PD. We synthesized several urea and thiourea analogues with a central 1,4-phenyl diurea/thiourea linkage and evaluated their effectiveness in reducing α-syn aggregation with a special focus on the selective inhibition of oligomer formation among other proteins. We utilized biophysical methods such as thioflavin T (ThT) fluorescence assays, transmission electron microscopy (TEM), photoinduced cross-linking of unmodified proteins (PICUP), as well as M17D intracellular inclusion cell-based assays to evaluate the antiaggregation properties and cellular protection of our best compounds. Our results identified compound 1 as the best compound in reducing α-syn fibril formation via ThT assays. The antioligomer formation of compound 1 was subsequently superseded by compound 2. Both compounds selectively curtailed the oligomer formation of α-syn but not tau 4R isoforms (0N4R, 2N4R) or p-tau (isoform 1N4R). Compounds 1 and 2 failed to abrogate tau 0N3R fibril formation by ThT and atomic force microscopy. Compound 2 was best at reducing the formation of recombinant α-syn fibrils by TEM. In contrast to compound 2, compound 1 reduced the formation of α-syn inclusions in M17D neuroblastoma cells in a dose-dependent manner. Compound 1 may provide molecular scaffolds for the optimization of symmetric molecules for its α-syn antiaggregation activity with potential therapeutic applications and development of small molecules in PD.
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Affiliation(s)
- Susantha
K. Ganegamage
- Department
of Basic Medical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, Indiana 47907, United States
| | - Eduardo Ramirez
- Department
of Basic Medical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, Indiana 47907, United States
| | - Heba Alnakhala
- Ann
Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women’s Hospital and Harvard Medical
School, Boston, Massachusetts 02115, United States
| | - Arati Tripathi
- Ann
Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women’s Hospital and Harvard Medical
School, Boston, Massachusetts 02115, United States
| | - Cuong Calvin Duc Nguyen
- Department
of Chemistry, College of Sciences, Purdue
University, West Lafayette, Indiana 47907, United States
| | - Ashique Zami
- Purdue
Institute for Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, Indiana 47907, United States
| | - Raluca Ostafe
- Purdue
Institute for Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, Indiana 47907, United States
| | - Shiliang Tian
- Department
of Chemistry, College of Sciences, Purdue
University, West Lafayette, Indiana 47907, United States
| | - Ulf Dettmer
- Ann
Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women’s Hospital and Harvard Medical
School, Boston, Massachusetts 02115, United States
| | - Jessica S. Fortin
- Department
of Basic Medical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, Indiana 47907, United States
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Shekar N, Vuong P, Kaur P. Analysing potent biomarkers along phytochemicals for breast cancer therapy: an in silico approach. Breast Cancer Res Treat 2024; 203:29-47. [PMID: 37726449 PMCID: PMC10771382 DOI: 10.1007/s10549-023-07107-7] [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: 06/22/2023] [Accepted: 08/23/2023] [Indexed: 09/21/2023]
Abstract
PURPOSE This research focused on the identification of herbal compounds as potential anti-cancer drugs, especially for breast cancer, that involved the recognition of Notch downstream targets NOTCH proteins (1-4) specifically expressed in breast tumours as biomarkers for prognosis, along with P53 tumour antigens, that were used as comparisons to check the sensitivity of the herbal bio-compounds. METHODS After investigating phytochemical candidates, we employed an approach for computer-aided drug design and analysis to find strong breast cancer inhibitors. The present study utilized in silico analyses and protein docking techniques to characterize and rank selected bio-compounds for their efficiency in oncogenic inhibition for use in precise carcinomic cell growth control. RESULTS Several of the identified phytocompounds found in herbs followed Lipinski's Rule of Five and could be further investigated as potential medicinal molecules. Based on the Vina score obtained after the docking process, the active compound Epigallocatechin gallate in green tea with NOTCH (1-4) and P53 proteins showed promising results for future drug repurposing. The stiffness and binding stability of green tea pharmacological complexes were further elucidated by the molecular dynamic simulations carried out for the highest scoring phytochemical ligand complex. CONCLUSION The target-ligand complex of green tea active compound Epigallocatechin gallate with NOTCH (1-4) had the potential to become potent anti-breast cancer therapeutic candidates following further research involving wet-lab experiments.
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Affiliation(s)
- Nivruthi Shekar
- UWA School of Agriculture and Environment, University of Western Australia, 35-Stirling Highway, Perth, WA, 6009, Australia
| | - Paton Vuong
- UWA School of Agriculture and Environment, University of Western Australia, 35-Stirling Highway, Perth, WA, 6009, Australia
| | - Parwinder Kaur
- UWA School of Agriculture and Environment, University of Western Australia, 35-Stirling Highway, Perth, WA, 6009, Australia.
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Akinboade MW, Egbemhenghe AU, Abdulkareem TO, Ibrahim IA, Omotara BS, Aderemi OE, Egejuru WA, Ajala CF, Meejay Kanu I, Oluwafemi OO, Aderemi CO, Ddamulira C, Afuape AR, Adekola AT, Ojeyemi T, Otuomagie OI. Identification of promising small-molecule inhibitors targeting STK17B for cancer therapeutics: molecular docking and molecular dynamics investigations. J Biomol Struct Dyn 2023:1-8. [PMID: 38147404 DOI: 10.1080/07391102.2023.2296605] [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: 06/10/2023] [Accepted: 10/02/2023] [Indexed: 12/28/2023]
Abstract
Cancer is a complex disease characterized by the uncontrolled growth of abnormal cells, leading to the formation of tumours. STK17B, a member of the DAPK family, has been implicated in various cancers and is considered a potential therapeutic target. However, no drug in the market has been approved for the treatment of STK17 B-associated cancer disease. This research aimed to identify direct inhibitors of STK17B using computational techniques. Ligand-based virtual screening and molecular docking were performed, resulting in the selection of three lead compounds (CID_135698391, CID_135453100, CID_136599608) with superior binding affinities compared to the reference compound dovitinib. While molecular docking simulation revealed specific interactions between the lead compounds and key amino acid residues at the binding pocket of STK17B, molecular dynamics simulations demonstrated that CID_135453100 and CID_136599608 exhibit stable conformations and comparable flexibility to dovitinib. However, CID_135698391 did not perform well using this metric as it displayed poor stability. Overall, small-molecule compounds CID_135453100 and CID_136599608 showed promising binding interactions and stability, suggesting their potential as direct inhibitors of STK17B. These findings could contribute to the exploration of novel therapeutic options targeting STK17B in cancer treatment.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | | | | | - Bamidele Samson Omotara
- Department of Chemistry and Chemical Engineering, University of New Haven, West Haven, CT, USA
| | - Olajide Enoch Aderemi
- Department of Chemistry and Chemical Engineering, University of New Haven, West Haven, CT, USA
| | | | | | - Ihunanya Meejay Kanu
- Department of Epidemiology and Biotatistics, Jackson State University, Jackson, MS, USA
| | | | | | | | | | | | - Toluwalase Ojeyemi
- Department of Environmental Toxicology, Texas Tech University, Lubbock, TX, USA
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Wu J, Lv J, Zhao L, Zhao R, Gao T, Xu Q, Liu D, Yu Q, Ma F. Exploring the role of microbial proteins in controlling environmental pollutants based on molecular simulation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167028. [PMID: 37704131 DOI: 10.1016/j.scitotenv.2023.167028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 09/03/2023] [Accepted: 09/10/2023] [Indexed: 09/15/2023]
Abstract
Molecular simulation has been widely used to study microbial proteins' structural composition and dynamic properties, such as volatility, flexibility, and stability at the microscopic scale. Herein, this review describes the key elements of molecular docking and molecular dynamics (MD) simulations in molecular simulation; reviews the techniques combined with molecular simulation, such as crystallography, spectroscopy, molecular biology, and machine learning, to validate simulation results and bridge information gaps in the structure, microenvironmental changes, expression mechanisms, and intensity quantification; illustrates the application of molecular simulation, in characterizing the molecular mechanisms of interaction of microbial proteins with four different types of contaminants, namely heavy metals (HMs), pesticides, dyes and emerging contaminants (ECs). Finally, the review outlines the important role of molecular simulations in the study of microbial proteins for controlling environmental contamination and provides ideas for the application of molecular simulation in screening microbial proteins and incorporating targeted mutagenesis to obtain more effective contaminant control proteins.
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Affiliation(s)
- Jieting Wu
- School of Environmental Science, Liaoning University, Shenyang 110036, China
| | - Jin Lv
- School of Environmental Science, Liaoning University, Shenyang 110036, China
| | - Lei Zhao
- State Key Laboratory of Urban Water Resources & Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Ruofan Zhao
- School of Environment, Beijing Normal University, Beijing 100875, China
| | - Tian Gao
- Key Laboratory of Integrated Regulation and Resource Development of Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, China
| | - Qi Xu
- PetroChina Fushun Petrochemical Company, Fushun 113000, China
| | - Dongbo Liu
- School of Environmental Science, Liaoning University, Shenyang 110036, China
| | - Qiqi Yu
- School of Environmental Science, Liaoning University, Shenyang 110036, China
| | - Fang Ma
- State Key Laboratory of Urban Water Resources & Environment, Harbin Institute of Technology, Harbin 150090, China.
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18
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Zhang C, Liu J, Sui Y, Liu S, Yang M. In silico drug repurposing carvedilol and its metabolites against SARS-CoV-2 infection using molecular docking and molecular dynamic simulation approaches. Sci Rep 2023; 13:21404. [PMID: 38049492 PMCID: PMC10696093 DOI: 10.1038/s41598-023-48398-6] [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: 08/18/2023] [Accepted: 11/26/2023] [Indexed: 12/06/2023] Open
Abstract
The pandemic of coronavirus disease 2019 (COVID-19) caused by the infection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a significant impact on the economy and public health worldwide. Therapeutic options such as drugs and vaccines for this newly emerged disease are eagerly desired due to the high mortality. Using the U.S. Food and Drug Administration (FDA) approved drugs to treat a new disease or entirely different diseases, in terms of drug repurposing, minimizes the time and cost of drug development compared to the de novo design of a new drug. Drug repurposing also has some other advantages such as reducing safety evaluation to accelerate drug application on time. Carvedilol, a non-selective beta-adrenergic blocker originally designed to treat high blood pressure and manage heart disease, has been shown to impact SARS-CoV-2 infection in clinical observation and basic studies. Here, we applied computer-aided approaches to investigate the possibility of repurposing carvedilol to combat SARS-CoV-2 infection. The molecular mechanisms and potential molecular targets of carvedilol were identified by evaluating the interactions of carvedilol with viral proteins. Additionally, the binding affinities of in vivo metabolites of carvedilol with selected targets were evaluated. The docking scores for carvedilol and its metabolites with RdRp were - 10.0 kcal/mol, - 9.8 kcal/mol (1-hydroxyl carvedilol), - 9.7 kcal/mol (3-hydroxyl carvedilol), - 9.8 kcal/mol (4-hydroxyl carvedilol), - 9.7 kcal/mol (5-hydroxyl carvedilol), - 10.0 kcal/mol (8-hydroxyl carvedilol), and - 10.1 kcal/mol (O-desmethyl carvedilol), respectively. Using the molecular dynamics simulation (100 ns) method, we further confirmed the stability of formed complexes of RNA-dependent RNA polymerase (RdRp) and carvedilol or its metabolites. Finally, the drug-target interaction mechanisms that contribute to the complex were investigated. Overall, this study provides the molecular targets and mechanisms of carvedilol and its metabolites as repurposed drugs to fight against SARS-CoV-2 infection.
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Affiliation(s)
- Chunye Zhang
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65212, USA
| | - Jiazheng Liu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau, 999078, China
| | - Yuxiang Sui
- School of Life Science, Shanxi Normal University, Linfen, 041004, Shanxi, China
| | - Shuai Liu
- The First Affiliated Hospital, Zhejiang University, Hangzhou, 310006, Zhejiang, China
| | - Ming Yang
- Department of Surgery, University of Missouri, Columbia, MO, 65212, USA.
- NextGen Precision Health Institution, University of Missouri, Columbia, MO, 65212, USA.
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Abouleisa RRE, Miller JM, Gebreil A, Salama ABM, Dwenger M, Abdelhafez H, Wahid RM, Adewumi AT, Soliman ME, Abo-Dya NE, Mohamed TMA. A novel small molecule inhibitor of p38⍺ MAP kinase augments cardiomyocyte cell cycle entry in response to direct cell cycle stimulation. Br J Pharmacol 2023; 180:3271-3289. [PMID: 37547998 PMCID: PMC10726296 DOI: 10.1111/bph.16209] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 06/21/2023] [Accepted: 07/12/2023] [Indexed: 08/08/2023] Open
Abstract
BACKGROUND AND PURPOSE Myocardial infarction (MI) is the leading cause of mortality globally due in part to the limited ability of cardiomyocytes (CMs) to regenerate. Recently, we demonstrated that overexpression of four-cell cycle factors, CDK1, CDK4, cyclin B1 and cyclin D1 (4F), induced cell division in ~20% of the post-mitotic CMs overexpressed 4F. The current study aims to identify a small molecule that augments 4F-induced CM cycle induction. EXPERIMENTAL APPROACH, KEY RESULTS Screening of small molecules with a potential to augment 4F-induced cell-cycle induction in 60-day-old mature human induced pluripotent cardiomyocytes (hiPS-CMs) revealed N-(4,6-Dimethylpyridin-2-yl)-4-(pyridine-4-yl)piperazine-1-carbothioamide (NDPPC), which activates cell cycle progression in 4F-transduced hiPS-CMs. Autodock tool and Autodock vina computational methods showed that NDPPC has a potential interaction with the binding site at the human p38⍺ mitogen-activated protein kinase (p38⍺ MAP kinase), a critical negative regulator of the mammalian cell cycle. A p38 MAP kinase activity assay showed that NDPPC inhibits p38⍺ with 5-10 times lower IC50 compared to the other P38 isoforms in a dose-dependent manner. Overexpression of p38⍺ MAP kinase in CMs inhibited 4F cell cycle induction, and treatment with NDPPC reversed the cell cycle inhibitory effect. CONCLUSION AND IMPLICATIONS NDPPC is a novel inhibitor for p38 MAP kinase and is a promising drug to augment CM cell cycle response to the 4F. NDPPC could become an adjunct treatment with other cell cycle activators for heart failure treatment.
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Affiliation(s)
- Riham R E Abouleisa
- Institute of Molecular Cardiology, Division of Cardiovascular Medicine, Department of Medicine, University of Louisville, Louisville, KY
| | - Jessica M. Miller
- Institute of Molecular Cardiology, Division of Cardiovascular Medicine, Department of Medicine, University of Louisville, Louisville, KY
| | - Ahmad Gebreil
- Institute of Molecular Cardiology, Division of Cardiovascular Medicine, Department of Medicine, University of Louisville, Louisville, KY
| | - Abou Bakr M. Salama
- Institute of Molecular Cardiology, Division of Cardiovascular Medicine, Department of Medicine, University of Louisville, Louisville, KY
- Department of Cardiovascular Medicine, Faculty of Medicine, Zagazig University, Egypt
| | - Marc Dwenger
- Institute of Molecular Cardiology, Division of Cardiovascular Medicine, Department of Medicine, University of Louisville, Louisville, KY
| | - Hania Abdelhafez
- Institute of Molecular Cardiology, Division of Cardiovascular Medicine, Department of Medicine, University of Louisville, Louisville, KY
| | - Reham M. Wahid
- Institute of Molecular Cardiology, Division of Cardiovascular Medicine, Department of Medicine, University of Louisville, Louisville, KY
- Physiology Department, Faculty of Medicine, Zagazig University, Egypt
| | - Adeniyi T. Adewumi
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
| | - Mahmoud E.S. Soliman
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
| | - Nader E. Abo-Dya
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Tabuk, Tabuk 71491, Saudi Arabia
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
| | - Tamer M A Mohamed
- Institute of Molecular Cardiology, Division of Cardiovascular Medicine, Department of Medicine, University of Louisville, Louisville, KY
- Division of Environmental Medicine, Department of Medicine, University of Louisville, Louisville, KY
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Hessel SS, Dwivany FM, Zainuddin IM, Wikantika K, Celik I, Emran TB, Tallei TE. A computational simulation appraisal of banana lectin as a potential anti-SARS-CoV-2 candidate by targeting the receptor-binding domain. J Genet Eng Biotechnol 2023; 21:148. [PMID: 38015308 PMCID: PMC10684481 DOI: 10.1186/s43141-023-00569-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 10/26/2023] [Indexed: 11/29/2023]
Abstract
BACKGROUND The ongoing concern surrounding coronavirus disease 2019 (COVID-19) primarily stems from continuous mutations in the genome of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), leading to the emergence of numerous variants. The receptor-binding domain (RBD) in the S1 subunit of the S protein of the virus plays a crucial role in recognizing the host's angiotensin-converting enzyme 2 (hACE2) receptor and facilitating cell membrane fusion processes, making it a potential target for preventing viral entrance into cells. This research aimed to determine the potential of banana lectin (BanLec) proteins to inhibit SARS-CoV-2 attachment to host cells by interacting with RBD through computational modeling. MATERIALS AND METHODS The BanLecs were selected through a sequence analysis process. Subsequently, the genes encoding BanLec proteins were retrieved from the Banana Genome Hub database. The FGENESH online tool was then employed to predict protein sequences, while web-based tools were utilized to assess the physicochemical properties, allergenicity, and toxicity of BanLecs. The RBDs of SARS-CoV-2 were modeled using the SWISS-MODEL in the following step. Molecular docking procedures were conducted with the aid of ClusPro 2.0 and HDOCK web servers. The three-dimensional structures of the docked complexes were visualized using PyMOL. Finally, molecular dynamics simulations were performed to investigate and validate the interactions of the complexes exhibiting the highest interactions, facilitating the simulation of their dynamic properties. RESULTS The BanLec proteins were successfully modeled based on the RNA sequences from two species of banana (Musa sp.). Moreover, an amino acid modification in the BanLec protein was made to reduce its mitogenicity. Theoretical allergenicity and toxicity predictions were conducted on the BanLecs, which suggested they were likely non-allergenic and contained no discernible toxic domains. Molecular docking analysis demonstrated that both altered and wild-type BanLecs exhibited strong affinity with the RBD of different SARS-CoV-2 variants. Further analysis of the molecular docking results showed that the BanLec proteins interacted with the active site of RBD, particularly the key amino acids residues responsible for RBD's binding to hACE2. Molecular dynamics simulation indicated a stable interaction between the Omicron RBD and BanLec, maintaining a root-mean-square deviation (RMSD) of approximately 0.2 nm for a duration of up to 100 ns. The individual proteins also had stable structural conformations, and the complex demonstrated a favorable binding-free energy (BFE) value. CONCLUSIONS These results confirm that the BanLec protein is a promising candidate for developing a potential therapeutic agent for combating COVID-19. Furthermore, the results suggest the possibility of BanLec as a broad-spectrum antiviral agent and highlight the need for further studies to examine the protein's safety and effectiveness as a potent antiviral agent.
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Affiliation(s)
- Sofia Safitri Hessel
- School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, West Java, 40132, Indonesia
| | - Fenny Martha Dwivany
- School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, West Java, 40132, Indonesia.
| | - Ima Mulyama Zainuddin
- Department of Biosystems, KU Leuven, Willem de Croylaan 42 box 2455, B-3001, Leuven, Belgium
| | - Ketut Wikantika
- Remote Sensing and Geographical Information Science Research Group, Faculty of Earth Science and Technology (FITB), Institut Teknologi Bandung, Bandung, West Java, 40132, Indonesia
| | - Ismail Celik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University, 38039, Kayseri, Turkey
| | - Talha Bin Emran
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI 02912, USA
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, 1207, Bangladesh
- Legorreta Cancer Center, Brown University, Providence, RI 02912, USA
| | - Trina Ekawati Tallei
- Department of Biology, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado, North Sulawesi, 95115, Indonesia.
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Gogoi N, Rudrapal M, Celik I, Kaishap PP, Chetia D. In vitro and in silico guided identification of antimalarial phytoconstituent(s) in the root of Citrus maxima (Burm.) Merr. J Biomol Struct Dyn 2023:1-12. [PMID: 37975318 DOI: 10.1080/07391102.2023.2283154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023]
Abstract
As a part of our continuous effort to find new therapeutic agents from natural sources, the hydroalcoholic (1:1) extract of Citrus maxima (Burm.) Merr. root was selected for the identification of possible antimalarial phytoconstituents. From the extract, three flavonoids including luteolin were isolated and evaluated for in vitro antimalarial activity against the chloroquine-sensitive (Pf3D7) and resistant (PfRKL-9) strains of Plasmodium falciparum. Among these, luteolin (CM3) showed the highest antimalarial activity with IC50 values of 2.315 ± 0.489 and 2.691 ± 0.454 µg/ml against the Pf3D7 and PfRKL-9 strains respectively. To assess the safety of luteolin (CM3), a cytotoxicity study against a normal human embryonic kidney cell line (HEK-293) was performed and the compound was found to be safe with a CC50 value of 222.3 ± 1.443 µg/ml. The docking study against 26 target proteins of P. falciparum revealed that luteolin (CM3) has a better binding affinity with two proteins, viz. P. falciparum lactate dehydrogenase (PfLDG) and P. falciparum enoyl-ACP reductase (PfEAR) in comparison to the co-crystallized ligands. Furthermore, the molecular dynamics simulation study of the protein-ligand complexes also supported the binding affinity and interactions of luteolin (CM3) at the active sites. Finally, the binding free energy calculation revealed that the luteolin formed a thermodynamically more stable complex with PfLDG (-50.955 ± 17.184 kJ/mol) than PfEAR (-24.856 ± 13.739 kJ/mol). Overall, in this study, we identified an antimalarial marker in the hydroalcoholic extract of C. maxima root which may act by inhibiting PfLDG.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Neelutpal Gogoi
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh, Assam, India
| | - Mithun Rudrapal
- Department of Pharmaceutical Sciences, School of Biotechnology and Pharmaceutical Sciences, Vignan's Foundation for Science, Technology & Research (Deemed to be University), Guntur, Andhra Pradesh, India
| | - Ismail Celik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University, Kayseri, Turkey
| | | | - Dipak Chetia
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh, Assam, India
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22
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Motahar SFS, Tiyoula FN, Motamedi E, Zeinalabedini M, Kavousi K, Ariaeenejad S. Computational Insights into the Selecting Mechanism of α-Amylase Immobilized on Cellulose Nanocrystals: Unveiling the Potential of α-Amylases Immobilized for Efficient Poultry Feed Hydrolysis. Bioconjug Chem 2023; 34:2034-2048. [PMID: 37823388 DOI: 10.1021/acs.bioconjchem.3c00304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
The selection of an appropriate amylase for hydrolysis poultry feed is crucial for achieving improved digestibility and high-quality feed. Cellulose nanocrystals (CNCs), which are known for their high surface area, provide an excellent platform for enzyme immobilization. Immobilization greatly enhances the operational stability of α-amylases and the efficiency of starch bioconversion in poultry feeds. In this study, we immobilized two metagenome-derived α-amylases, PersiAmy2 and PersiAmy3, on CNCs and employed computational methods to characterize and compare the degradation efficiencies of these enzymes for poultry feed hydrolysis. Experimental in vitro bioconversion assessments were performed to validate the computational outcomes. Molecular docking studies revealed the superior hydrolysis performance of PersiAmy3, which displayed stronger electrostatic interactions with CNCs. Experimental characterization demonstrated the improved performance of both α-amylases after immobilization at high temperatures (80 °C). A similar trend was observed under alkaline conditions, with α-amylase activity reaching 88% within a pH range of 8.0 to 9.0. Both immobilized α-amylases exhibited halotolerance at NaCl concentrations up to 3 M and retained over 50% of their initial activity after 13 use cycles. Notably, PersiAmy3 displayed more remarkable improvements than PersiAmy2 following immobilization, including a significant increase in activity from 65 to 80.73% at 80 °C, an increase in activity to 156.48% at a high salinity of 3 M NaCl, and a longer half-life, indicating greater thermal stability within the range of 60 to 80 °C. These findings were substantiated by the in vitro hydrolysis of poultry feed, where PersiAmy3 generated 53.53 g/L reducing sugars. This comprehensive comparison underscores the utility of computational methods as a faster and more efficient approach for selecting optimal enzymes for poultry feed hydrolysis, thereby providing valuable insights into enhancing feed digestibility and quality.
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Affiliation(s)
- Seyedeh Fatemeh Sadeghian Motahar
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj 31535-1897, Iran
| | - Fereshteh Noroozi Tiyoula
- Laboratory of Complex Biological Systems and Bioinformatics (CBB), Department of Bioinformatics, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran 14176-14411, Iran
| | - Elaheh Motamedi
- Department of Nanotechnology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Research and Extension Organization (AREEO), Karaj 55555, Iran
| | - Mehrshad Zeinalabedini
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj 31535-1897, Iran
| | - Kaveh Kavousi
- Laboratory of Complex Biological Systems and Bioinformatics (CBB), Department of Bioinformatics, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran 14176-14411, Iran
| | - Shohreh Ariaeenejad
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj 31535-1897, Iran
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23
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Arfat Y, Zafar I, Sehgal SA, Ayaz M, Sajid M, Khan JM, Ahsan M, Rather MA, Khan AA, Alshehri JM, Akash S, Nepovimova E, Kuca K, Sharma R. In silico designing of multiepitope-based-peptide (MBP) vaccine against MAPK protein express for Alzheimer's disease in Zebrafish. Heliyon 2023; 9:e22204. [PMID: 38058625 PMCID: PMC10695983 DOI: 10.1016/j.heliyon.2023.e22204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 10/24/2023] [Accepted: 11/06/2023] [Indexed: 12/08/2023] Open
Abstract
Understanding the role of the mitogen-activated protein kinases (MAPKs) signalling pathway is essential in advancing treatments for neurodegenerative disorders like Alzheimer's. In this study, we investigate in-silico techniques involving computer-based methods to extract the MAPK1 sequence. Our applied methods enable us to analyze the protein's structure, evaluate its properties, establish its evolutionary relationships, and assess its prevalence in populations. We also predict epitopes, assess their ability to trigger immune responses, and check for allergenicity using advanced computational tools to understand their immunological properties comprehensively. We apply virtual screening, docking, and structure modelling to identify promising drug candidates, analyze their interactions, and enhance drug design processes. We identified a total of 30 cell-targeting molecules against the MAPK1 protein, where we selected top 10 CTL epitopes (PAGGGPNPG, GGGPNPGSG, SAPAGGGPN, AVSAPAGGG, AGGGPNPGS, ATAAVSAPA, TAAVSAPAG, ENIIGINDI, INDIIRTPT, and NDIIRTPTI) for further evaluation to determine their potential efficacy, safety, and suitability for vaccine design based on strong binding potential. The potential to cover a large portion of the world's population with these vaccines is substantial-88.5 % for one type and 99.99 % for another. In exploring the molecular docking analyses, we examined a library of compounds from the ZINC database. Among them, we identified twelve compounds with the lowest binding energy. Critical residues in the MAPK1 protein, such as VAL48, LYS63, CYS175, ASP176, LYS160, ALA61, LEU165, TYR45, SER162, ARG33, PRO365, PHE363, ILE40, ASN163, and GLU42, are pivotal for interactions with these compounds. Our result suggests that these compounds could influence the protein's behaviour. Moreover, our docking analyses revealed that the predicted peptides have a strong affinity for the MAPK1 protein. These peptides form stable complexes, indicating their potential as potent inhibitors. This study contributes to the identification of new drug compounds and the screening of their desired properties. These compounds could potentially help reduce the excessive activity of MAPK1, which is linked to Alzheimer's disease.
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Affiliation(s)
- Yasir Arfat
- Department of Biotechnology, Faculty of Life Sciences, University of Okara, Okara, 56300, Pakistan
| | - Imran Zafar
- Department of Bioinformatics and Computational Biology, Virtual University, Punjab, 54700, Pakistan
| | - Sheikh Arslan Sehgal
- Department of Bioinformatics, Institute of Biochemistry, Biotechnology and Bioinformatics, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Mazhar Ayaz
- Department of Parasitology, Faculty of Veterinary Science, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, Pakistan
| | - Muhammad Sajid
- Department of Biotechnology, Faculty of Life Sciences, University of Okara, Okara, 56300, Pakistan
| | - Jamal Muhammad Khan
- Department of Parasitology, Faculty of Veterinary Science, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, Pakistan
| | - Muhammad Ahsan
- Department of Environmental Sciences, Institute of Environmental and Agricultural Sciences, University of Okara, Okara, 56300, Pakistan
| | - Mohd Ashraf Rather
- Division of Fish Genetics and Biotechnology, Faculty of Fisheries, Rangil- Gandarbal (SKAUST-K), India
| | - Azmat Ali Khan
- Pharmaceutical Biotechnology Laboratory, Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Jamilah M. Alshehri
- Pharmaceutical Biotechnology Laboratory, Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Shopnil Akash
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International, University, Dhaka, Bangladesh
| | - Eugenie Nepovimova
- Department of Chemistry, Faculty of Science, University of Hradec Králové, Hradec Králové, 50 003, Czech Republic
| | - Kamil Kuca
- Department of Chemistry, Faculty of Science, University of Hradec Králové, Hradec Králové, 50 003, Czech Republic
- Biomedical Research Center, University Hospital Hradec Kralove, 50005, Hradec Kralove, Czech Republic
| | - Rohit Sharma
- Department of Rasashastra and Bhaishajya Kalpana, Faculty of Ayurveda, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
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24
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Kaur H, Kalia M, Singh V, Taneja N. Identification of novel inhibitors against Escherichia coli utilizing HisC as a target from histidine biosynthesis pathway. J Biomol Struct Dyn 2023; 41:9907-9914. [PMID: 36416560 DOI: 10.1080/07391102.2022.2148319] [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: 05/16/2022] [Accepted: 11/10/2022] [Indexed: 11/24/2022]
Abstract
Escherichia coli is a gram-negative bacterial pathogen that poses a significant challenge both clinically and epidemiologically. Large numbers of multi-drug resistant E. coli have emerged in the last decade, because of the selection pressure generated by the inadequate use of antibiotics. Although research to combat antibiotic resistance has been going on extensively but still lags in the rate of development of newer antibiotics. Therefore, newer approaches are required to speed up the rate of discovery of antibiotics. Computational methods for screening of inhibitors have made a significant contribution to the discovery of novel antimicrobials. The present study utilized histidinol-phospho aminotransferase (HisC) as a target. HisC is an enzyme that plays a crucial role in the biosynthesis of histidine and its absence in mammals makes it an attractive drug target. A ZINC library of 5000 natural compounds was screened against HisC (PDB ID: 1FG7) using PyRx and the first 500 hits were selected for secondary screening after sorting the result on the basis of binding score. Fifteen compounds passed the secondary filter ADME and out of these five passed toxicity filters; the best among five hits was selected on the basis of its binding score and inhibition constants. Further, molecular dynamics simulations and free binding were computed of selected five compounds and two natural compounds ZINC402598829 and ZINC31157928 complexed with HisC were found as highly stable. Overall, our results indicated that these natural sources could be used as potential HisC inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Harpreet Kaur
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Manmohit Kalia
- Department of Biology, State University of New York, Binghamton, NY, USA
| | - Vikram Singh
- School of Computational Biology and Bioinformatics, Central University of Himachal Pradesh, Dharamshala, Himachal Pradesh, India
| | - Neelam Taneja
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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25
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Hermanto FE, Warsito W, Rifa'i M, Widodo N. Understanding hypocholesterolemic activity of soy isoflavones: Completing the puzzle through computational simulations. J Biomol Struct Dyn 2023; 41:9931-9937. [PMID: 36443895 DOI: 10.1080/07391102.2022.2148752] [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: 03/14/2022] [Accepted: 11/12/2022] [Indexed: 11/30/2022]
Abstract
The hypocholesterolemic activity of soy isoflavones has been studied, but the exact mechanism underlying the activity remains unclear. This study reveals the proposed mechanism of the cholesterol-lowering effect of soy isoflavones by computational simulations. Daidzin, Glycitin, Genistin, Daidzein, Glycitein, Genistein, Glyceollin I, Glyceollin II, and Glyceollin III were selected to be analyzed their interaction with 3-Hydroxy-3-Methyl-Glutaryl-Coenzyme A Reductase (HMGCR) and Sterol Regulatory Element-Binding Protein 2 (SREBP2) as key factors in cholesterol biosynthesis as well as Proprotein Convertase Subtilisin/Kexin type 9 (PCSK9) as a common target for hypercholesterolemia. Protein-isoflavones interaction was analyzed using AutoDock. According to binding energy calculations, a total of five out of those nine isoflavones, including Glycitin, Genistin, Genistein, Glyceollin II, and Glyceollin III, were favored to be a HMGCR inhibitor but not with SREBP2 and PCSK9. Those isoflavones were then compared with Simvastatin as known inhibitor of HMGCR. Isoflavone with binding energy lower than Simvastatin then directed to molecular dynamics using YASARA and headed into toxicity estimations. Almost all of those isoflavones could bind with HMGCR with better stability than Simvastatin according to molecular dynamics simulations. Toxicity prediction filtered two out of the five isoflavones mentioned earlier as the proper candidate to be an HMGCR inhibitor. Those isoflavones were Genistin and Genistein. In summary, the hypocholesterolemic activity of soy isoflavones may occur by blocking the cholesterol biosynthesis pathway.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Feri Eko Hermanto
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Brawijaya, Malang, Indonesia
| | - Warsito Warsito
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Brawijaya, Malang, Indonesia
- Essential Oil Institute, Universitas Brawijaya, Malang, Indonesia
| | - Muhaimin Rifa'i
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Brawijaya, Malang, Indonesia
- Biosystem Study Center, Universitas Brawijaya, Malang, Indonesia
| | - Nashi Widodo
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Brawijaya, Malang, Indonesia
- Biosystem Study Center, Universitas Brawijaya, Malang, Indonesia
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26
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Roy S, Roy S, Mahata B, Pramanik J, Hennrich ML, Gavin AC, Teichmann SA. CLICK-chemoproteomics and molecular dynamics simulation reveals pregnenolone targets and their binding conformations in Th2 cells. Front Immunol 2023; 14:1229703. [PMID: 38022565 PMCID: PMC10644475 DOI: 10.3389/fimmu.2023.1229703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 10/05/2023] [Indexed: 12/01/2023] Open
Abstract
Pregnenolone (P5) is synthesized as the first bioactive steroid in the mitochondria from cholesterol. Clusters of differentiation 4 (CD4+) and Clusters of differentiation 8 (CD8+) immune cells synthesize P5 de novo; P5, in turn, play important role in immune homeostasis and regulation. However, P5's biochemical mode of action in immune cells is still emerging. We envisage that revealing the complete spectrum of P5 target proteins in immune cells would have multifold applications, not only in basic understanding of steroids biochemistry in immune cells but also in developing new therapeutic applications. We employed a CLICK-enabled probe to capture P5-binding proteins in live T helper cell type 2 (Th2) cells. Subsequently, using high-throughput quantitative proteomics, we identified the P5 interactome in CD4+ Th2 cells. Our study revealed P5's mode of action in CD4+ immune cells. We identified novel proteins from mitochondrial and endoplasmic reticulum membranes to be the primary mediators of P5's biochemistry in CD4+ and to concur with our earlier finding in CD8+ immune cells. Applying advanced computational algorithms and molecular simulations, we were able to generate near-native maps of P5-protein key molecular interactions. We showed bonds and interactions between key amino acids and P5, which revealed the importance of ionic bond, hydrophobic interactions, and water channels. We point out that our results can lead to designing of novel molecular therapeutics strategies.
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Affiliation(s)
- Sougata Roy
- Department of Biology, Ashoka University, Rajiv Gandhi Education City, Sonipat, Haryana, India
| | - Sudeep Roy
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czechia
| | - Bidesh Mahata
- Division of Immunology, Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Jhuma Pramanik
- Division of Immunology, Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Marco L. Hennrich
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, EMBL, Heidelberg, Germany
- Cellzome, a GlaxoSmithKline (GSK) company, Genomic Sciences, Pharma R&D, Heidelberg, Germany
| | - Anne-Claude Gavin
- Department for Cell Physiology and Metabolism, Centre Medical Universitaire, University of Geneva, Geneva, Switzerland
- Diabetes Center, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Sarah A. Teichmann
- Cellular Genetics, Wellcome Sanger Institute, Cambridge, United Kingdom
- Theory of Condensed Matter, Cavendish Laboratory, Cambridge, United Kingdom
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27
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de Almeida GC, de Oliveira GB, da Silva Monte Z, Costa ÉCS, da Silva Falcão EP, Scotti L, Scotti MT, Oliveira Silva R, Pereira VRA, da Silva ED, Junior PAS, de Andrade Cavalcante MK, de Melo SJ. Structure-based design, optimization of lead, synthesis, and biological evaluation of compounds active against Trypanosoma cruzi. Chem Biol Drug Des 2023; 102:843-856. [PMID: 37455325 DOI: 10.1111/cbdd.14294] [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: 10/13/2022] [Revised: 04/18/2023] [Accepted: 07/05/2023] [Indexed: 07/18/2023]
Abstract
Chagas' disease affects approximately eight million people throughout the world, especially the poorest individuals. The protozoan that causes this disease-Trypanosoma cruzi-has the enzyme cruzipain, which is the main therapeutic target. As no available medications have satisfactory effectiveness and safety, it is of fundamental importance to design and synthesize novel analogues that are more active and selective. In the present study, molecular docking and the in silico prediction of ADMET properties were used as strategies to optimize the trypanocidal activity of the pyrimidine compound ZN3F based on interactions with the target site in cruzipain. From the computational results, eight 4-amino-5-carbonitrile-pyrimidine analogues were proposed, synthesized (5a-f and 7g-h) and, tested in vitro on the trypomastigote form of the Tulahuen strain of T. cruzi. The in silico study showed that the designed analogues bond favorably to important amino acid residues of the active site in cruzipain. An in vitro evaluation of cytotoxicity was performed on L929 mammal cell lines. All derivatives inhibited the Tulahuen strain of T. cruzi and also exhibited lower toxicity to L929 cells. The 5e product, in particular, proved to be a potent, selective (IC50 = 2.79 ± 0.00 μM, selectivity index = 31.3) inhibitor of T. cruzi. The present results indicated the effectiveness of drugs based on the structure of the receptor, revealing the potential trypanocidal of pyrimidines. This study also provides information on molecular aspects for the inhibition of cruzipain.
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Affiliation(s)
- Gleybson Correia de Almeida
- Postgraduate Program in Pharmaceutical Sciences, Department of Pharmaceutical Sciences, Federal University of Pernambuco/UFPE, Recife, Brazil
| | - Gerliny Bezerra de Oliveira
- Postgraduate Program in Pharmaceutical Sciences, Department of Pharmaceutical Sciences, Federal University of Pernambuco/UFPE, Recife, Brazil
| | - Zenaide da Silva Monte
- Postgraduate Program in Pharmaceutical Sciences, Department of Pharmaceutical Sciences, Federal University of Pernambuco/UFPE, Recife, Brazil
| | - Érick Caique Santos Costa
- Postgraduate Program in Biological Sciences, Department of Biosciences, Federal University of Pernambuco/UFPE, Recife, Brazil
| | | | - Luciana Scotti
- Laboratory of Cheminformatics, Program of Natural and Synthetic Bioactive Products (PgPNSB), Health Sciences Center, Federal University of Paraíba, João Pessoa, Brazil
| | - Marcus Tullius Scotti
- Laboratory of Cheminformatics, Program of Natural and Synthetic Bioactive Products (PgPNSB), Health Sciences Center, Federal University of Paraíba, João Pessoa, Brazil
| | - Ricardo Oliveira Silva
- Department of Fundamental Chemistry, Center for Exact and Natural Sciences, Federal University of Pernambuco, Av. Journalist Anibal Fernandes, Recife, Brazil
| | - Valéria Rêgo Alves Pereira
- Aggeu Magalhães Research Center, Oswaldo Cruz Foundation, Federal University of Pernambuco - Campus da Av. Prof. Moraes Rego, Recife, Brazil
| | - Elis Dionisio da Silva
- Aggeu Magalhães Research Center, Oswaldo Cruz Foundation, Federal University of Pernambuco - Campus da Av. Prof. Moraes Rego, Recife, Brazil
| | - Policarpo Ademar Sales Junior
- Aggeu Magalhães Research Center, Oswaldo Cruz Foundation, Federal University of Pernambuco - Campus da Av. Prof. Moraes Rego, Recife, Brazil
| | - Marton Kaique de Andrade Cavalcante
- Aggeu Magalhães Research Center, Oswaldo Cruz Foundation, Federal University of Pernambuco - Campus da Av. Prof. Moraes Rego, Recife, Brazil
| | - Sebastião José de Melo
- Postgraduate Program in Pharmaceutical Sciences, Department of Pharmaceutical Sciences, Federal University of Pernambuco/UFPE, Recife, Brazil
- Postgraduate Program in Biological Sciences, Department of Biosciences, Federal University of Pernambuco/UFPE, Recife, Brazil
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28
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Rocha Aguiar G, Leda Gomes de Lemos T, Braz-Filho R, Marques da Fonseca A, Silva Marinho E, Vasconcelos Ribeiro PR, Marques Canuto K, Queiroz Monte FJ. Synthesis and in silico study of chenodeoxycholic acid and its analogues as an alternative inhibitor of spike glycoprotein of SARS-CoV-2. J Biomol Struct Dyn 2023; 41:8334-8348. [PMID: 36218138 DOI: 10.1080/07391102.2022.2133010] [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: 06/07/2022] [Accepted: 09/30/2022] [Indexed: 10/17/2022]
Abstract
COVID-19, caused by SARS-CoV-2, is a viral infection that has generated one of the most significant health problems in the world. Spike glycoprotein is a crucial enzyme in viral replication and transcription mediation. There are reports in the literature on using bile acid in the fight against this virus through in vitro tests. This work presents the synthesis of nine chenodeoxycholic acid derivatives (1-9), which were prepared by oxidation, acetylation, formylation, and esterification reactions, and the analogs 6-9 have not yet been reported in the literature and the possibility of conducting an in silico study of bile acid derivatives as a therapeutic alternative to combat the virus using glycoprotein as a macromolecular target. As a result, five compounds (1, 6-9) possessed favorable competitive interactions with the lowest energies compared to the native ligand (BLA), and the highlighted compound 9 got the best scores. At the same time, analog 1 presented the best ADME filter result. Molecular dynamics also simulated these compounds to verify their stability within the active protein site to seek new therapeutic propositions to fight against the pandemic. Physical and spectroscopic data have fully characterized all the compounds.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Gisele Rocha Aguiar
- Departamento de Química Orgânica, Universidade Federal do Ceará, Fortaleza-CE, Brazil
| | | | - Raimundo Braz-Filho
- Laboratório de Ciências Químicas, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Rio de Janeiro-RJ, Brazil
| | - Aluísio Marques da Fonseca
- Instituto de Ciências Exatas e Naturais, Universidade da Integração Internacional da Lusofonia Afro-Brasileira, Redenção-CE, Brazil
| | - Emmanuel Silva Marinho
- Faculdade de Filosofia Dom Aureliano Matos, Universidade Estadual do Ceará, Limoeiro do Norte-CE, Brazil
| | | | - Kirley Marques Canuto
- Laboratório multiusuário de Química de Produtos Naturais, Embrapa Agroindústria Tropical, Fortaleza-CE, Brazil
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29
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Mohamed AAR, Moustafa GG, El Bohy KM, Saber TM, Metwally MMM, El Desoukey Mohammed H, El-Far AH, Alotaibi BS, Alosaimi M, Abuzahrah SS, Alqahtani LS. Exploring cardiac impact of oral nicotine exposure in a transplantable Neoplasm Mice Model: Insights from biochemical analysis, morphometry, and molecular docking: Chlorella vulgaris green algae support. Toxicology 2023; 497-498:153629. [PMID: 37704175 DOI: 10.1016/j.tox.2023.153629] [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: 07/24/2023] [Revised: 09/02/2023] [Accepted: 09/05/2023] [Indexed: 09/15/2023]
Abstract
Nicotine-induced cardiac tissue damage is a concern for cancer patients, but the exact pathogenesis from nicotine oral exposure is unclear. This study was designed to investigate the impact of nicotine and Chlorella vulgaris (Ch. V) on cardiac glutathione homeostasis, inflammatory response, cardiac damage markers, apoptotic proteins and histopathological findings in an experimentally transplantable neoplasm mouse model (Ehrlich ascites carcinoma; EAC). In the in-vivo experiment, the female Swiss mice were divided into four groups: control, Ch.V (100 mg/kg), Nicotine (100 µg/ml/kg), and a combination group ( Nocotine+ Ch.V) for 40 days. Furthermore, in this study,the effects of C. vulgaris components on caspase-3, TNF-α, and IL-1β activity were explored using Molecular Operating Environment (MOE) docking software to ensure its ability to counteract the toxic effects of nicotine. The results indicated that nicotine has induced significant (P < 0.001) cardiopathic alterations in EAC-bearing mice with changes in cardiac tissue enzymes. C. Vulgaris attenuated the nicotine-induced cardiac glutathione inhibition, suppressed the inflammatory response, exerted antiapoptotic effects, mitigated myocardial injury biomarkers, and repaired cellular and tissue damage. Moreover, the molecular docking results revealed the ability of C. vulgaris to bind with interleukin-1 receptor type 1 (IL1R1) and tumor necrosis factor receptor superfamily member 1 A (TNFRSF1A) in the mice tissues, ameliorating apoptosis and inflammatory processes associated with nicotine-induced cardiotoxicity. This study provides a model for understanding nicotine-induced myocardial injury during experimentally transplantable neoplasm. It highlights C. vulgaris as a beneficial food supplement for cancer patients exposed to nicotine orally.
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Affiliation(s)
- Amany Abdel-Rahman Mohamed
- Department of Forensic Medicine and Toxicology, Faculty of Veterinary Medicine, Zagazig University, Zagazig 44519, Egypt
| | - Gihan G Moustafa
- Department of Forensic Medicine and Toxicology, Faculty of Veterinary Medicine, Zagazig University, Zagazig 44519, Egypt
| | - Khlood M El Bohy
- Department of Forensic Medicine and Toxicology, Faculty of Veterinary Medicine, Zagazig University, Zagazig 44519, Egypt
| | - Taghred M Saber
- Department of Forensic Medicine and Toxicology, Faculty of Veterinary Medicine, Zagazig University, Zagazig 44519, Egypt
| | - Mohamed M M Metwally
- Department of pathology and clinical pathology, faculty of veterinary medicine, King Salman international University, Ras sudr، Egypt; Department of Pathology, Faculty of Veterinary Medicine, Zagazig University, Zagazig 44511, Egypt
| | - Heba El Desoukey Mohammed
- Specialist of Forensic Medicine and Toxicology, Veterinary Services, El Senbellawein, Dakahlia Governorate, Egypt
| | - Ali H El-Far
- Department of Biochemistry, Faculty of Veterinary Medicine, Damanhour University, Damanhour 22511, Egypt
| | - Badriyah S Alotaibi
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia.
| | - Manal Alosaimi
- Department of Basic Health Sciences, College of Medicine, Princess Nourah bint Abdulrahman University, P.O Box 84428, Riyadh 11671, Saudi Arabia
| | - Samah S Abuzahrah
- Department of Biological Sciences, College of Science, University of Jeddah, 21959, Saudi Arabia
| | - Leena S Alqahtani
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah 23445, Saudi Arabia
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30
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Atiya A, Alsayari A, Bin Muhsinah A, Almaghaslah D, Bilgrami AL, Abdulmonem WA, Alorfi NM, DasGupta D, Ashraf GM, Shamsi A, Shahwan M. Role of lisinopril in the therapeutic management of cardiovascular disease by targeting microtubule affinity regulating kinase 4: molecular docking and molecular dynamics simulation approaches. J Biomol Struct Dyn 2023; 41:8824-8830. [PMID: 36376029 DOI: 10.1080/07391102.2022.2143425] [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: 09/15/2022] [Accepted: 10/13/2022] [Indexed: 11/16/2022]
Abstract
Cardiovascular diseases (CVDs) are a major cause of premature adult death. Various factors contribute to the development of CVDs, such as atherosclerosis leading to myocardial infarction (MI), and compromised cardiac function after MI leads to chronic heart failure with systemic health complications and a high mortality rate. Microtubule detyrosination has rapidly evolved as an essential mechanism to regulate cardiomyocyte contractility. Microtubule affinity regulating kinase 4 (MARK4) regulates cardiomyocyte contractility in a way that it promotes phosphorylation of microtubule-associated protein 4, thereby facilitating the access of vasohibin 2-a tubulin carboxypeptidase-to microtubules for the detyrosination of α-tubulin. Lisinopril, a drug belonging to the class of angiotensin-converting enzyme inhibitors, is used to treat high blood pressure. This is also used to treat heart failure, which plays a vital role in improving the survival rate post-heart attack. In this study, we will evaluate the MARK4 inhibitory potential of lisinopril employing molecular docking and molecular dynamics (MD) simulation approaches. Molecular docking analysis suggested that lisinopril binds to MARK4 with a significant binding affinity forming interactions with functionally essential residues of MARK4. Additionally, MD simulation deciphered the structural dynamics and stability of the MARK4-lisinopril complex. The findings of MD studies established that minimal structural deviations are observed during simulation, affirming the stability of the MARK4-lisinopril complex. Altogether, this study demonstrates lisinopril's crucial role in the therapeutic management of CVD by targeting MARK4.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Akhtar Atiya
- Department of Pharmacognosy, College of Pharmacy, King Khalid University (KKU), Abha, Saudi Arabia
| | - Abdulrhman Alsayari
- Department of Pharmacognosy, College of Pharmacy, King Khalid University (KKU), Abha, Saudi Arabia
- Complementary and Alternative Medicine Unit, King Khalid University (KKU), Abha, Saudi Arabia
| | - Abdullatif Bin Muhsinah
- Department of Pharmacognosy, College of Pharmacy, King Khalid University (KKU), Abha, Saudi Arabia
- Complementary and Alternative Medicine Unit, King Khalid University (KKU), Abha, Saudi Arabia
| | - Dalia Almaghaslah
- Department of Clinical Pharmacy, College of Pharmacy, King Khalid University (KKU), Abha, Saudi Arabia
| | - Anwar L Bilgrami
- Deanship of Scientific Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Waleed Al Abdulmonem
- Department of Pathology, College of Medicine, Qassim University, Buraydah, Saudi Arabia
| | - Nasser M Alorfi
- Department of Pharmacology and Toxicology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Debarati DasGupta
- College of Pharmacy, University of Michigan, Ann Arbor, Michigan, USA
| | - Ghulam Md Ashraf
- Department of Medical Laboratory Sciences, College of Health Sciences, University of Sharjah, University City, Sharjah, United Arab Emirates
| | - Anas Shamsi
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
- Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, United Arab Emirates
| | - Moyad Shahwan
- Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, United Arab Emirates
- College of Pharmacy & Health Sciences, Ajman University, Ajman, United Arab Emirates
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31
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Umar AH, Ratnadewi D, Rafi M, Sulistyaningsih YC, Hamim H, Kusuma WA. Drug candidates and potential targets of Curculigo spp. compounds for treating diabetes mellitus based on network pharmacology, molecular docking and molecular dynamics simulation. J Biomol Struct Dyn 2023; 41:8544-8560. [PMID: 36300505 DOI: 10.1080/07391102.2022.2135597] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 10/08/2022] [Indexed: 10/31/2022]
Abstract
Curculigo spp. is a herb that is commonly used in Indonesia to treat diabetes mellitus (DM) . The main active components of Curculigo spp. were identified through our previous metabolomic study and online database platform. However, the biological mechanisms underlying Curculigo spp. activity in treating DM remain unclear. Therefore, in this study, a network pharmacology was used to explore the active compounds of Curculigo spp. and their potential molecular mechanisms for treating DM. Oral bioavailability and drug-likeness from the compounds of Curculigo spp. were screened using Lipinski's rule of five, BBB, HIA + and Caco-2 permeability criteria. A network of compound-target-disease-pathway was then constructed using Cytoscape. The highest degree compounds and targets were then confirmed by molecular docking and molecular dynamics (MD) simulations. The human body can absorb 33 compounds derived from Curculigo spp. In addition, 58 nodes and 62 edges generated a network analysis with the DM target. The highest degree of the compound-target-disease pathway was for orcinol glucoside, AKR1B1, autoimmune diabetes, bile acid and bile salt metabolism. Furthermore, the computational docking method on Curculigo spp. compounds with the highest degree revealed that orcinol glucoside interacted with PTPN1 through a hydrogen bond and resulted in a binding energy of -7.2 kcal mol-1. Through hydrogen bonds, orcinol glucoside in PTPN1 regulates multiple signaling pathways via the adherens junction pathway, which may play a therapeutic role in DM (type 2 diabetes: obesity). In addition, MD simulation confirmed that orcinol glucoside, is suitable for DM treatment by interacting with PTPN1.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Abdul Halim Umar
- Division of Pharmaceutical Biology, College of Pharmaceutical Sciences Makassar (Sekolah Tinggi Ilmu Farmasi Makassar), Makassar, Indonesia
| | - Diah Ratnadewi
- Department of Biology, Faculty of Mathematics and Natural Sciences, IPB University, Bogor, Indonesia
| | - Mohamad Rafi
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, IPB University, Bogor, Indonesia
| | | | - Hamim Hamim
- Department of Biology, Faculty of Mathematics and Natural Sciences, IPB University, Bogor, Indonesia
| | - Wisnu Ananta Kusuma
- Department of Computer Science, Faculty of Mathematics and Natural Sciences, IPB University, Bogor, Indonesia
- Tropical Biopharmaca Research Center, IPB University, Bogor, Indonesia
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32
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Tian Y, Zhao G, Cheng M, Lu L, Zhang H, Huang X. A nitroreductase DnrA catalyzes the biotransformation of several diphenyl ether herbicides in Bacillus sp. Za. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12647-5. [PMID: 37395748 DOI: 10.1007/s00253-023-12647-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/03/2023] [Accepted: 06/10/2023] [Indexed: 07/04/2023]
Abstract
Diphenyl ether herbicides, typical globally used herbicides, threaten the agricultural environment and the sensitive crops. The microbial degradation pathways of diphenyl ether herbicides are well studied, but the nitroreduction of diphenyl ether herbicides by purified enzymes is still unclear. Here, the gene dnrA, encoding a nitroreductase DnrA responsible for the reduction of nitro to amino groups, was identified from the strain Bacillus sp. Za. DnrA had a broad substrate spectrum, and the Km values of DnrA for different diphenyl ether herbicides were 20.67 μM (fomesafen), 23.64 μM (bifenox), 26.19 μM (fluoroglycofen), 28.24 μM (acifluorfen), and 36.32 μM (lactofen). DnrA also mitigated the growth inhibition effect on cucumber and sorghum through nitroreduction. Molecular docking revealed the mechanisms of the compounds fomesafen, bifenox, fluoroglycofen, lactofen, and acifluorfen with DnrA. Fomesafen showed higher affinities and lower binding energy values for DnrA, and residue Arg244 affected the affinity between diphenyl ether herbicides and DnrA. This research provides new genetic resources and insights into the microbial remediation of diphenyl ether herbicide-contaminated environments. KEY POINTS: • Nitroreductase DnrA transforms the nitro group of diphenyl ether herbicides. • Nitroreductase DnrA reduces the toxicity of diphenyl ether herbicides. • The distance between Arg244 and the herbicides is related to catalytic efficiency.
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Affiliation(s)
- Yanning Tian
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Guoqiang Zhao
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Minggen Cheng
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Luyao Lu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Hao Zhang
- College of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, 473061, People's Republic of China
| | - Xing Huang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
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33
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Cohen H, Wani NA, Ben Hur D, Migliolo L, Cardoso MH, Porat Z, Shimoni E, Franco OL, Shai Y. Interaction of Pexiganan (MSI-78)-Derived Analogues Reduces Inflammation and TLR4-Mediated Cytokine Secretion: A Comparative Study. ACS OMEGA 2023; 8:17856-17868. [PMID: 37251186 PMCID: PMC10210221 DOI: 10.1021/acsomega.3c00850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 04/28/2023] [Indexed: 05/31/2023]
Abstract
Antibiotic-resistant bacterial infections have increased the prevalence of sepsis and septic shock mortality worldwide and have become a global concern. Antimicrobial peptides (AMPs) show remarkable properties for developing new antimicrobial agents and host response modulatory therapies. A new series of AMPs derived from pexiganan (MSI-78) were synthesized. The positively charged amino acids were segregated at their N- and C-termini, and the rest of the amino acids created a hydrophobic core surrounded by positive charges and were modified to simulate the lipopolysaccharide (LPS). The peptides were investigated for their antimicrobial activity and LPS-induced cytokine release inhibition profile. Various biochemical and biophysical methods were used, including attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy, microscale thermophoresis (MST), and electron microscopy. Two new AMPs, MSI-Seg-F2F and MSI-N7K, preserved their neutralizing endotoxin activity while reducing toxicity and hemolytic activity. Combining all of these properties makes the designed peptides potential candidates to eradicate bacterial infection and detoxify LPS, which might be useful for sepsis treatment.
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Affiliation(s)
- Hadar Cohen
- Department
of Biomolecular Sciences, The Weizmann Institute
of Science, Rehovot 76100, Israel
| | - Naiem Ahmad Wani
- Department
of Biomolecular Sciences, The Weizmann Institute
of Science, Rehovot 76100, Israel
| | - Daniel Ben Hur
- Department
of Biomolecular Sciences, The Weizmann Institute
of Science, Rehovot 76100, Israel
| | - Ludovico Migliolo
- Departamento
de Engenharia Sanitária e Ambiental, Universidade Católica Dom Bosco, Campo Grande 79117-900, Brazil
| | - Marlon H. Cardoso
- S-Inova,
Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande 79117900, MS, Brazil
- Centro
de
Análises Proteômicas e Bioquímicas, Pós-Graduação
em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília 70790160, DF, Brazil
- Instituto
de Biociências (INBIO), Universidade
Federal de Mato Grosso do Sul, Cidade Universitária, Campo Grande 79070900, Mato Grosso do Sul, Brazil
| | - Ziv Porat
- The
Department of Life Sciences Core Facilities, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Eyal Shimoni
- Department
of Chemical Research Support, The Weizmann
Institute of Science, Rehovot 76100, Israel
| | - Octavio Luiz Franco
- Departamento
de Engenharia Sanitária e Ambiental, Universidade Católica Dom Bosco, Campo Grande 79117-900, Brazil
- S-Inova,
Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande 79117900, MS, Brazil
- Centro
de
Análises Proteômicas e Bioquímicas, Pós-Graduação
em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília 70790160, DF, Brazil
| | - Yechiel Shai
- Department
of Biomolecular Sciences, The Weizmann Institute
of Science, Rehovot 76100, Israel
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Widyawati T, Syahputra RA, Syarifah S, Sumantri IB. Analysis of Antidiabetic Activity of Squalene via In Silico and In Vivo Assay. Molecules 2023; 28:molecules28093783. [PMID: 37175192 PMCID: PMC10180456 DOI: 10.3390/molecules28093783] [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: 03/15/2023] [Revised: 04/10/2023] [Accepted: 04/20/2023] [Indexed: 05/15/2023] Open
Abstract
Squalene has been tested widely in pharmacological activity including anticancer, antiinflammatory, antioxidant, and antidiabetic properties. This study aims to examine antidiabetic activity of squalene in silico and in vivo models. In the in silico model, the PASS server was used to evaluate squalene antidiabetic properties. Meanwhile, the in vivo model was conducted on a Type 2 Diabetes Mellitus (T2DM) with the rats separated into three groups. These include squalene (160 mg/kgbw), metformin (45 mg/kgbw), and diabetic control (DC) (aquades 10 mL/kgbw) administered once daily for 14 days. Fasting Blood Glucose Level (FBGL), Dipeptidyl Peptidase IV (DPPIV), leptin, and Superoxide Dismutase (SOD) activity were measured to analysis antidiabetic and antioxidant activity. Additionally, the pancreas was analysed through histopathology to examine the islet cell. The results showed that in silico analysis supported squalene antidiabetic potential. In vivo experiment demonstrated that squalene decreased FBGL levels to 134.40 ± 16.95 mg/dL. The highest DPPIV level was in diabetic control- (61.26 ± 15.06 ng/mL), while squalene group showed the lowest level (44.09 ± 5.29 ng/mL). Both metformin and squalene groups showed minor pancreatic rupture on histopathology. Leptin levels were significantly higher (p < 0.05) in diabetic control group (15.39 ± 1.77 ng/mL) than both squalene- (13.86 ± 0.47 ng/mL) and metformin-treated groups (9.22 ± 0.84 ng/mL). SOD activity were higher in both squalene- and metformin-treated group, particularly 22.42 ± 0.27 U/mL and 22.81 ± 0.08 U/mL than in diabetic control (21.88 ± 0.97 U/mL). In conclusion, in silico and in vivo experiments provide evidence of squalene antidiabetic and antioxidant properties.
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Affiliation(s)
- Tri Widyawati
- Department of Pharmacology and Therapeutic, Faculty of Medicine, Universitas Sumatera Utara, Medan 20155, Sumatera Utara, Indonesia
| | - Rony Abdi Syahputra
- Department of Pharmacology, Faculty of Pharmacy, Universitas Sumatera Utara, Medan 20155, Sumatera Utara, Indonesia
| | - Siti Syarifah
- Department of Pharmacology and Therapeutic, Faculty of Medicine, Universitas Sumatera Utara, Medan 20155, Sumatera Utara, Indonesia
| | - Imam Bagus Sumantri
- Department of Pharmaceutical Biology, Faculty of Pharmacy, Universitas Sumatera Utara, Medan 20155, Sumatera Utara, Indonesia
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35
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Chiang YT, Xiao YB, Hsu SH, Chang SW, Chou CC. Molecular interactions of tannic acid and matrix metalloproteinases 2 and 9. Comput Struct Biotechnol J 2023; 21:2792-2800. [PMID: 37181658 PMCID: PMC10172635 DOI: 10.1016/j.csbj.2023.04.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 04/13/2023] [Accepted: 04/13/2023] [Indexed: 05/16/2023] Open
Abstract
Tannic acid (TA) has antibacterial, antioxidant, and anti-inflammatory properties and acts as an adhesive, hemostatic, and crosslinking agent in hydrogels. Matrix metalloproteinases (MMPs), a family of endopeptidase enzymes, play important roles in tissue remodeling and wound healing. TA has been reported to inhibit MMP-2/- 9 activities, thereby improving both tissue remodeling and wound healing. However, the mechanism of interaction of TA with MMP-2 and MMP-9 has not been fully elucidated. In this study, the full atomistic modeling approach was applied to explore the mechanisms and structures of TA binding with MMP-2 and MMP-9. Macromolecular models of the TA-MMP-2/- 9 complex were built by docking based on experimentally resolved MMP structures, and further equilibrium processes were examined by molecular dynamics (MD) simulations to investigate the binding mechanism and structural dynamics of the TA-MMP-2/- 9 complexes. The molecular interactions between TA and MMPs, including H-bond formation and hydrophobic and electrostatic interactions, were analyzed and decoupled to elucidate the dominant factors in TA-MMP binding. TA binds to MMPs mainly at two binding regions, residues 163-164 and 220-223 in MMP-2 and residues 179-190 and 228-248 in MMP-9. Two arms of TA participate in binding MMP-2 with 3.61 hydrogen bonds. On the other hand, TA binds MMP-9 with a distinct configuration involving four arms with 4.75 hydrogen bonds, resulting in a tighter binding conformation. Understanding the binding mechanism and structural dynamics of TA with these two MMPs provides crucial and fundamental knowledge regarding the inhibitory and stabilizing effects of TA on MMPs.
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Affiliation(s)
- Ya-Tang Chiang
- Institute of Polymer Science and Engineering, National Taiwan University, Roosevelt Road No. 1, Section 4, 10617 Taipei, Taiwan
| | - Yu-Bai Xiao
- Department of Civil Engineering, College of Engineering, National Taiwan University, Roosevelt Road No. 1, Section 4, 10617 Taipei, Taiwan
| | - Shan-hui Hsu
- Institute of Polymer Science and Engineering, National Taiwan University, Roosevelt Road No. 1, Section 4, 10617 Taipei, Taiwan
| | - Shu-Wei Chang
- Department of Civil Engineering, College of Engineering, National Taiwan University, Roosevelt Road No. 1, Section 4, 10617 Taipei, Taiwan
- Department of Biomedical Engineering, College of Engineering, National Taiwan University, Roosevelt Road No. 1, Section 4, 10617 Taipei, Taiwan
| | - Chia-Ching Chou
- Institute of Applied Mechanics, College of Engineering, National Taiwan University, Roosevelt Road No. 1, Section 4, 10617 Taipei, Taiwan
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36
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Dipankar P, Kumar P, Sarangi PP. In silico identification and characterization of small-molecule inhibitors specific to RhoG/Rac1 signaling pathway. J Biomol Struct Dyn 2023; 41:560-580. [PMID: 34877916 DOI: 10.1080/07391102.2021.2009032] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Rho family GTPases serve as molecular switches in numerous cellular processes, and their overexpression is involved in disease conditions. RhoG is one of the less explored Rho GTPases with significant sequential and structural homology with Rac1. Experimental mutations in RhoG (i.e., RhoGG12V and RhoGQ61L) are shown to dysregulate cell migration. Thus, targeting upstream activators of RhoG, such as guanine nucleotide exchange factors (GEFs), maybe an important strategy for inhibiting RhoG activation. In the current study, we have modelled the 3D structure of RhoG with greater accuracy as confirmed through PROCHECK, ProSA, and Verify3D. Our results indicate that 90.4% of residues are in the Ramachandran plots favoured region, with the Z-score of -6.46, and 87.96% of residues had an averaged 3D-1D score ≥0.2. Further, we have evaluated and binding dynamics of ten Rac1 inhibitors to investigate their potential to inhibit RhoG by targeting GEFs binding grooves. To this end, the binding energy of the docked complexes of the wild-type (WT) RhoG and its mutant proteins with inhibitor molecules was calculated using the MM/PBSA method. Our results from docking studies showed that macrolide1 binds efficiently with the GEF site of WT RhoG and the mutants mentioned above. However, an extensive analysis using MD simulations (200 ns) showed that the Rac1 based inhibitor, EHop-016, and NSC23766 might bind with greater affinity to GEF sites of mutants and WT RhoG. Thus, the results from the study indicate that Rac1 inhibitors have the potential for use as therapeutics in conditions involving dysregulation of RhoG.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Pankaj Dipankar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Puneet Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Pranita P Sarangi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
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37
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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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Albaqami FF, Altharawi A, Althurwi HN, Alharthy KM, Qasim M, Muhseen ZT, Tahir ul Qamar M. Computational Modeling and Evaluation of Potential mRNA and Peptide-Based Vaccine against Marburg Virus (MARV) to Provide Immune Protection against Hemorrhagic Fever. BIOMED RESEARCH INTERNATIONAL 2023; 2023:5560605. [PMID: 37101690 PMCID: PMC10125739 DOI: 10.1155/2023/5560605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 01/22/2023] [Accepted: 02/21/2023] [Indexed: 04/28/2023]
Abstract
A hemorrhagic fever caused by the Marburg virus (MARV) belongs to the Filoviridae family and has been classified as a risk group 4 pathogen. To this day, there are no approved effective vaccinations or medications available to prevent or treat MARV infections. Reverse vaccinology-based approach was formulated to prioritize B and T cell epitopes utilizing a numerous immunoinformatics tools. Potential epitopes were systematically screened based on various parameters needed for an ideal vaccine such as allergenicity, solubility, and toxicity. The most suitable epitopes capable of inducing immune response were shortlisted. Epitopes with population coverage of 100% and fulfilling set parameters were selected for docking with human leukocyte antigen molecules, and binding affinity of each peptide was analyzed. Finally, 4 CTL and HTL each while 6 B cell 16-mers were used for designing multiepitope subunit (MSV) and mRNA vaccine joined via suitable linkers. Immune simulations were used to validate the constructed vaccine's capacity to induce a robust immune response whereas molecular dynamics simulations were used to confirm epitope-HLA complex stability. Based on these parameter's studies, both the vaccines constructed in this study offer a promising choice against MARV but require further experimental verification. This study provides a rationale point to begin with the development of an efficient vaccine against Marburg virus; however, the findings need further experimental validation to confirm the computational finding of this study.
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Affiliation(s)
- Faisal F. Albaqami
- Department of Pharmacology, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Ali Altharawi
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Hassan N. Althurwi
- Department of Pharmacology, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Khalid M. Alharthy
- Department of Pharmacology, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Muhammad Qasim
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad 38000, Pakistan
| | - Ziyad Tariq Muhseen
- Department of Pharmacy, Al-Mustaqbal University College, Hillah, Babylon 51001, Iraq
| | - Muhammad Tahir ul Qamar
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad 38000, Pakistan
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Madhana Priya N, Balasundaram A, Sidharth Kumar N, Udhaya Kumar S, Thirumal Kumar D, Magesh R, Zayed H, George Priya Doss C. Controlling cell proliferation by targeting cyclin-dependent kinase 6 using drug repurposing approach. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 135:97-124. [PMID: 37061342 DOI: 10.1016/bs.apcsb.2023.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2023]
Abstract
Cyclin-dependent kinase 6 (CDK6) is an essential kinase in cell cycle progression, which is a viable target for inhibitors in various malignancies, including breast cancer. This study aimed to virtually screen efficient compounds as new leads in treating breast cancer using a drug repurposing approach. Apoptosis regulatory compounds were taken from the seleckchem database. Molecular docking experiments were carried out in the presence of abemaciclib, a routinely used FDA drug. Compared to conventional drugs, the two compounds demonstrated a higher binding affinity for CDK6. Compounds (N-benzyl-6-[(4-hydroxyphenyl)methyl]-8-(naphthalen-1-ylmethyl)-4,7-dioxo-3,6,9,9a-tetrahydro-2H-pyrazino[1,2-a]pyrimidine-1-carboxamide) and (1'-[4-[1-(4-fluorophenyl)indol-3-yl]butyl]spiro[1H-2-benzofuran-3,4'-piperidine]) were discovered to have an inhibitory effect against CDK6 at -8.49 and -6.78kcal/mol, respectively, compared to -8.09kcal/mol of the control molecule, the interacting residues of these two new compounds were found to fall within the binding site of the CDK6 molecule. Both compounds exhibited equal ADME features compared with abemaciclib and would be well distributed and metabolized by the body with an appropriate druglikeness range. Lastly, molecular dynamics was initiated for 200ns for the selected potent inhibitors and abemaciclib as complexed with CDK6. The RMSD, RMSF, Rg, H-Bond interactions, SASA, PCA, FEL, and MM/PBSA analysis were performed for the complexes to assess the stability, fluctuations, radius of gyration, hydrogen bond interaction, solvent accessibility, essential dynamics, free energy landscape, and MM/PBSA. The selected two compounds are small molecules in the appropriate druglikeness range. The results observed in molecular docking and molecular dynamics simulations were most promising for two compounds, suggesting their potent inhibitory effect against CDK6. We propose that these candidate compounds can undergo in vitro validation and in vivo testing for their further use against cancer.
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Farasati Far B, Asadi S, Naimi-Jamal MR, Abdelbasset WK, Aghajani Shahrivar A. Insights into the interaction of azinphos-methyl with bovine serum albumin: experimental and molecular docking studies. J Biomol Struct Dyn 2022; 40:11863-11873. [PMID: 34427168 DOI: 10.1080/07391102.2021.1968954] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In the present study, combining spectroscopic and molecular modeling techniques has been used to analyze azinphos-methyl binding properties, as an organophosphorus pesticide, to bovine serum albumin. The quenching interaction of azinphos-methyl with bovine serum albumin was investigated in an appropriate physiological state (pH = 7.4). Fluorescence spectroscopy, UV-visible spectroscopy, circular dichroism (CD) and Fourier transform infrared spectroscopy (FTIR). Findings showed differences in the secondary protein structure microenvironment following interaction with azinphos-methyl. The results from spectroscopic experiments suggest that azinphos-methyl binds to bovine serum albumin residues with a binding constant in the range of 0.099 × 105-0.209 × 105 M-1 in one binding site (Tyr 160). The experimental results are supported by computational techniques such as docking using a bovine serum albumin crystal model. The results show that azinphos-methyl is linked to the site I of bovine serum albumin (in subdomain IB), and the result was in accordance with the experimental result. Based on the negative ΔG°, ΔH° and ΔS° values, the binding between azinphos-methyl and bovine serum albumin was spontaneous, and docking studies confirmed hydrogen bonding and van der Waals forces between them.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Bahareh Farasati Far
- Research Laboratory of Green Organic Synthesis and Polymers, Department of Chemistry, Iran University of Science and Technology, Tehran, Iran
| | - Soada Asadi
- Department of Analytical Chemistry, Faculty of Chemistry, Urmia University, Urmia, Iran
| | - Mohammad Reza Naimi-Jamal
- Research Laboratory of Green Organic Synthesis and Polymers, Department of Chemistry, Iran University of Science and Technology, Tehran, Iran
| | - Walid Kamal Abdelbasset
- Department of Health and Rehabilitation Sciences, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al Kharj, Saudi Arabia.,Department of Physical Therapy, Kasr Al-Aini Hospital, Cairo University, Giza, Egypt
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41
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Ali MC, Khatun MS, Jahan SI, Das R, Munni YA, Rahman MM, Dash R. In silico design of epitope-based peptide vaccine against non-typhoidal Salmonella through immunoinformatic approaches. J Biomol Struct Dyn 2022; 40:10696-10714. [PMID: 36529187 DOI: 10.1080/07391102.2021.1947381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Non-typhoidal Salmonella (NTS) is one of the leading bacterial causes of many invasive human infections with a high antibiotic resistance profile. With this concern, the current study aimed to design an effective epitope-based peptide vaccine against NTS species as a successive and substitutive protective measure of invasive NTS disease. To design rationally, the current study considered a comprehensive in silico workflow combination of both immunoinformatics and molecular modeling approaches, including molecular docking and molecular dynamics (MD) simulation. We identified the two most promising T cell epitopes KVLYGIFAI and YGIFAITAL, and three B cell epitopes AAPVQVGEAAGS, TGGGDGSNT, and TGGGDGSNTGTTTT, in the outer membrane of NTS. Using these epitopes, a multiepitope vaccine was subsequently constructed along with appropriate adjuvant and linkers, which showed a good binding affinity and stability with toll-like receptor 2 (TLR2) in both molecular docking and MD simulation. Furthermore, in silico immune simulation described a strong immune response with a high number of antibodies, interferon-γ, and activated B and T cells. This study collectively suggests that predicted vaccine constructs could be considered potential vaccine candidates against common NTS species.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Md Chayan Ali
- Department of Biotechnology & Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, Bangladesh
| | - Mst Shanzeda Khatun
- Department of Biotechnology & Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, Bangladesh
| | - Sultana Israt Jahan
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Raju Das
- Department of Physiology, Dongguk University College of Medicine, Gyeongju, Republic of Korea
| | - Yeasmin Akter Munni
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju, Republic of Korea
| | - Md Mafizur Rahman
- Department of Biotechnology & Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, Bangladesh
| | - Raju Dash
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju, Republic of Korea
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42
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Arzani H, Rafii-Tabar H, Ramezani F. The investigation into the effect of the length of RGD peptides and temperature on the interaction with the αIIbβ3 integrin: a molecular dynamic study. J Biomol Struct Dyn 2022; 40:9701-9712. [PMID: 34060983 DOI: 10.1080/07391102.2021.1932602] [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: 12/16/2022]
Abstract
The tripeptide Arg-Gly-Asp acid (RGD) is a protein sequence in the binding of proteins to cell surfaces, and is involved in various biological processes such as cell adhesion to the extracellular matrix, platelet activation, hemostasis, etc. The C2 domain of the Von Willebrand Factor (VWF), containing the RGD motif, plays an important role in the initial homeostasis process. It binds to the αIIbβ3 integrin and stimulates platelet aggregation. We have investigated, using the molecular Dynamic (MD) simulation method, the effect of the RGD-peptide length, and temperature variation, on the binding to the αIIbβ3 integrin receptor. We examined 10 different structural modes of the αIIbβ3 at three different temperatures; 237 K, 310 K and 318 K. Our findings show that the amino acids that form a binding pocket include Asp224, Tyr234, Ser226, Tyr190, Tyr189, Trp260, Trp262, Asp259, Lys253, Arg214, Asp217, Ser161 and Ala218 and that the ligand-receptor interaction was increased at higher temperatures. It was also found that the increase in the number of ligands' amino acids and their types (% glycine) plays an important role in the stability, conformation, and ligand-receptor interaction.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hossein Arzani
- Department of Medical Physics and Biomedical Engineering, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hashem Rafii-Tabar
- Department of Medical Physics and Biomedical Engineering, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,The Physics Branch of Iran Academy of Sciences, Tehran, Iran
| | - Fatemeh Ramezani
- Physiology Research Center, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
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Bioinformatics Designing and Molecular Modelling of a Universal mRNA Vaccine for SARS-CoV-2 Infection. Vaccines (Basel) 2022; 10:vaccines10122107. [PMID: 36560516 PMCID: PMC9785986 DOI: 10.3390/vaccines10122107] [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: 11/01/2022] [Revised: 11/30/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022] Open
Abstract
At this present stage of COVID-19 re-emergence, designing an effective candidate vaccine for different variants of SARS-CoV-2 is a study worthy of consideration. This research used bioinformatics tools to design an mRNA vaccine that captures all the circulating variants and lineages of the virus in its construct. Sequences of these viruses were retrieved across the six continents and analyzed using different tools to screen for the preferable CD8+ T lymphocytes (CTL), CD4+ T lymphocytes (HTL), and B-cell epitopes. These epitopes were used to design the vaccine. In addition, several other co-translational residues were added to the construct of an mRNA vaccine whose molecular weight is 285.29686 kDa with an estimated pI of 9.2 and has no cross affinity with the human genome with an estimated over 68% to cover the world population. It is relatively stable, with minimal deformability in its interaction with the human innate immune receptor, which includes TLR 3 and TLR 9. The overall result has proven that the designed candidate vaccine is capable of modulating cell-mediated immune responses by activating the actions of CD4+ T cells, natural killer cells, and macrophages, and displayed an increased memory T cell and B cell activities, which may further be validated via in vivo and in vitro techniques.
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Balakrishnan V, Ganapathy S, Veerasamy V, Subramaniyan S, Mohamed Hussain SA, Duraisamy R. Modifying effects of nerolidol on cell surface glycoconjugates and suppressed inflammation during DMBA-induced oral carcinogenesis: An in vivo and in silico. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01260-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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45
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Althurwi HN, Alharthy KM, Albaqami FF, Altharawi A, Javed MR, Muhseen ZT, Tahir ul Qamar M. mRNA-Based Vaccine Designing against Epstein-Barr Virus to Induce an Immune Response Using Immunoinformatic and Molecular Modelling Approaches. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:13054. [PMID: 36293632 PMCID: PMC9602923 DOI: 10.3390/ijerph192013054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/03/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
Epstein-Barr Virus (EBV) is a human pathogen that has a morbidity rate of 90% in adults worldwide. Infectious mononucleosis is caused by EBV replication in B cells and epithelial cells of the host. EBV has also been related to autoimmune illnesses, including multiple sclerosis and cancers like nasopharyngeal carcinomas and Burkitt's lymphoma. Currently, no effective medications or vaccinations are available to treat or prevent EBV infection. Thus, the current study focuses on a bioinformatics approach to design an mRNA-based multi-epitope (MEV) vaccine to prevent EBV infections. For this purpose, we selected six antigenic proteins from the EBV proteome based on their role in pathogenicity to predict, extract, and analyze T and B cell epitopes using immunoinformatics tools. The epitopes were directed through filtering parameters including allergenicity, toxicity, antigenicity, solubility, and immunogenicity assessment, and finally, the most potent epitopes able to induce T and B cell immune response were selected. In silico molecular docking of prioritized T cell peptides with respective Human Leukocytes Antigens molecules, were carried out to evaluate the individual peptide's binding affinity. Six CTL, four HTL, and ten linear B cell epitopes fulfilled the set parameters and were selected for MEV-based mRNA vaccine. The prioritized epitopes were joined using suitable linkers to improve epitope presentation. The immune simulation results affirmed the designed vaccine's capacity to elicit a proper immune response. The MEV-based mRNA vaccine constructed in this study offers a promising choice for a potent vaccine against EBV.
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Affiliation(s)
- Hassan N. Althurwi
- Department of Pharmacology and Toxicology, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Khalid M. Alharthy
- Department of Pharmacology and Toxicology, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Faisal F. Albaqami
- Department of Pharmacology and Toxicology, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Ali Altharawi
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Muhammad Rizwan Javed
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad 38000, Pakistan
| | - Ziyad Tariq Muhseen
- Department of Pharmacy, Al-Mustaqbal University College, Hillah 51001, Babylon, Iraq
| | - Muhammad Tahir ul Qamar
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad 38000, Pakistan
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Camellia sinensis mediated synthesis and characterization of nanoparticles and applications to control Gram-negative ESBL producing antibiotic resistant bacterial pathogens. FOOD BIOSCI 2022. [DOI: 10.1016/j.fbio.2022.102070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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47
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Chen F, Zhou L, Zhou B, Zhang S, Ma X, Zhou H, Tuo X. Elucidation on the interaction between transferrin and ascorbic acid: A study based on spectroscopic analysis, molecular docking technology, and antioxidant evaluation. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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48
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Jaafar NR, Jailani N, Rahman RA, Öner ET, Murad AMA, Illias RM. Protein surface engineering and interaction studies of maltogenic amylase towards improved enzyme immobilisation. Int J Biol Macromol 2022; 213:70-82. [DOI: 10.1016/j.ijbiomac.2022.05.169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 05/14/2022] [Accepted: 05/24/2022] [Indexed: 11/30/2022]
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What Makes GPCRs from Different Families Bind to the Same Ligand? Biomolecules 2022; 12:biom12070863. [PMID: 35883418 PMCID: PMC9313020 DOI: 10.3390/biom12070863] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 06/09/2022] [Accepted: 06/19/2022] [Indexed: 12/10/2022] Open
Abstract
G protein-coupled receptors (GPCRs) are the largest class of cell-surface receptor proteins with important functions in signal transduction and often serve as therapeutic drug targets. With the rapidly growing public data on three dimensional (3D) structures of GPCRs and GPCR-ligand interactions, computational prediction of GPCR ligand binding becomes a convincing option to high throughput screening and other experimental approaches during the beginning phases of ligand discovery. In this work, we set out to computationally uncover and understand the binding of a single ligand to GPCRs from several different families. Three-dimensional structural comparisons of the GPCRs that bind to the same ligand revealed local 3D structural similarities and often these regions overlap with locations of binding pockets. These pockets were found to be similar (based on backbone geometry and side-chain orientation using APoc), and they correlate positively with electrostatic properties of the pockets. Moreover, the more similar the pockets, the more likely a ligand binding to the pockets will interact with similar residues, have similar conformations, and produce similar binding affinities across the pockets. These findings can be exploited to improve protein function inference, drug repurposing and drug toxicity prediction, and accelerate the development of new drugs.
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Chen YP, Wang KX, Cai JQ, Li Y, Yu HL, Wu Q, Meng W, Wang H, Yin CH, Wu J, Huang MB, Li R, Guan DG. Detecting Key Functional Components Group and Speculating the Potential Mechanism of Xiao-Xu-Ming Decoction in Treating Stroke. Front Cell Dev Biol 2022; 10:753425. [PMID: 35646921 PMCID: PMC9136080 DOI: 10.3389/fcell.2022.753425] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 02/25/2022] [Indexed: 02/05/2023] Open
Abstract
Stroke is a cerebrovascular event with cerebral blood flow interruption which is caused by occlusion or bursting of cerebral vessels. At present, the main methods in treating stroke are surgical treatment, statins, and recombinant tissue-type plasminogen activator (rt-PA). Relatively, traditional Chinese medicine (TCM) has widely been used at clinical level in China and some countries in Asia. Xiao-Xu-Ming decoction (XXMD) is a classical and widely used prescription in treating stroke in China. However, the material basis of effect and the action principle of XXMD are still not clear. To solve this issue, we designed a new system pharmacology strategy that combined targets of XXMD and the pathogenetic genes of stroke to construct a functional response space (FRS). The effective proteins from this space were determined by using a novel node importance calculation method, and then the key functional components group (KFCG) that could mediate the effective proteins was selected based on the dynamic programming strategy. The results showed that enriched pathways of effective proteins selected from FRS could cover 99.10% of enriched pathways of reference targets, which were defined by overlapping of component targets and pathogenetic genes. Targets of optimized KFCG with 56 components can be enriched into 166 pathways that covered 80.43% of 138 pathways of 1,012 pathogenetic genes. A component potential effect score (PES) calculation model was constructed to calculate the comprehensive effective score of components in the components-targets-pathways (C-T-P) network of KFCGs, and showed that ferulic acid, zingerone, and vanillic acid had the highest PESs. Prediction and docking simulations show that these components can affect stroke synergistically through genes such as MEK, NFκB, and PI3K in PI3K-Akt, cAMP, and MAPK cascade signals. Finally, ferulic acid, zingerone, and vanillic acid were tested to be protective for PC12 cells and HT22 cells in increasing cell viabilities after oxygen and glucose deprivation (OGD). Our proposed strategy could improve the accuracy on decoding KFCGs of XXMD and provide a methodologic reference for the optimization, mechanism analysis, and secondary development of the formula in TCM.
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Affiliation(s)
- Yu-peng Chen
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China,Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Southern Medical University, Guangzhou, China
| | - Ke-xin Wang
- Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Department of Neurosurgery, National Key Clinical Specialty/Engineering Technology Research Center of Education Ministry of China, Neurosurgery Institute, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Jie-qi Cai
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China,Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Southern Medical University, Guangzhou, China
| | - Yi Li
- Department of Radiology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Hai-lang Yu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China,Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Southern Medical University, Guangzhou, China
| | - Qi Wu
- Department of Burns, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Wei Meng
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China,Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Southern Medical University, Guangzhou, China
| | - Handuo Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China,Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Southern Medical University, Guangzhou, China
| | - Chuan-hui Yin
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China,Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Southern Medical University, Guangzhou, China
| | - Jie Wu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China,Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Southern Medical University, Guangzhou, China
| | - Mian-bo Huang
- Department of Histology and Embryology, Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China,*Correspondence: Mian-bo Huang, ; Rong Li, ; Dao-gang Guan,
| | - Rong Li
- Department of Cardiovascular Disease, First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China,*Correspondence: Mian-bo Huang, ; Rong Li, ; Dao-gang Guan,
| | - Dao-gang Guan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China,Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Southern Medical University, Guangzhou, China,*Correspondence: Mian-bo Huang, ; Rong Li, ; Dao-gang Guan,
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