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Sharma G, Kumar N, Sharma CS, Mishra SS. In silico guided screening of active components of C. lanceolata as 3-chymotrypsin-like protease inhibitors of novel coronavirus. 3 Biotech 2023; 13:324. [PMID: 37663751 PMCID: PMC10471561 DOI: 10.1007/s13205-023-03745-2] [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: 06/01/2023] [Accepted: 08/14/2023] [Indexed: 09/05/2023] Open
Abstract
Despite the intense worldwide efforts towards the identification of potential anti-CoV therapeutics, no antiviral drugs have yet been discovered. Numerous vaccines are now approved for use, but they all serve as preventative measures. To effectively treat viral infections, it is crucial to find new antiviral drugs that are derived from natural sources. Various compounds with potential activity against 3 chymotrypsin-like protease (3CLpro) were reported and some are validated by bioassay studies. Therefore, we performed the computational screening of phytoconstituents of Codonopsis lanceolata to search for potential antiviral hit candidates. The curated compounds of the plant C. lanceolata were collected and downloaded from the literature. The binding affinity of the curated datasets was predicted for the target 3CLpro. Stigmasterol exhibits the highest docking score for the 3CLpro target. In addition, molecular dynamics (MD) simulations were conducted for the validation of docking results using root mean square deviation and root mean square fluctuation plots. The MD results indicated that the docked complex was stable and retained hydrogen bonding and non-bonding interactions. Furthermore, the calculation of pharmacokinetic parameters and Lipinski's rule of five suggest that C. lanceolata has the potential for drug-likeness. In order to develop new medicines for this debilitating disease, we will focus on the primary virus-based and host-based targets that can direct medicinal chemists to identify novel treatments to produce new drugs for it. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03745-2.
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Affiliation(s)
- Ganesh Sharma
- Department of Pharmaceutical Chemistry, Bhupal Nobles’ College of Pharmacy, Bhupal Nobles’ University, Udaipur, 313002 India
| | - Neeraj Kumar
- Department of Pharmaceutical Chemistry, Bhupal Nobles’ College of Pharmacy, Bhupal Nobles’ University, Udaipur, 313002 India
| | - Chandra Shekhar Sharma
- Department of Pharmaceutical Chemistry, Bhupal Nobles’ College of Pharmacy, Bhupal Nobles’ University, Udaipur, 313002 India
| | - Shashank Shekher Mishra
- Faculty of Pharmacy, School of Pharmaceutical and Populations Health Informatics, DIT University, Dehradun, 248009 India
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Bhowmik D, Bhuyan A, Gunalan S, Kothandan G, Kumar D. In silico and immunoinformatics based multiepitope subunit vaccine design for protection against visceral leishmaniasis. J Biomol Struct Dyn 2023:1-22. [PMID: 37655736 DOI: 10.1080/07391102.2023.2252901] [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: 02/12/2023] [Accepted: 08/22/2023] [Indexed: 09/02/2023]
Abstract
Visceral leishmaniasis (VL) is a vector-borne neglected tropical protozoan disease with high fatality and no certified vaccine. Conventional vaccine preparation is challenging and tedious. Here in this work, we created a global multiepitope subunit vaccination against VL utilizing innovative immunoinformatics technique based on the extensively conserved epitopic regions of the PrimPol protein of Leishmania donovani consisting of four subunits which were analyzed and studied, out of which DNA primase large subunit and DNA polymerase α subunit B were evaluated as antigens by Vaxijen 2.0. The multiepitope vaccine design includes a single adjuvant β-defensins, eight CTL epitopes, eight HTL epitopes, seven linear BCL epitopes and one discontinuous BCL epitope to induce innate, cellular and humoral immune responses against VL. The Expasy ProtParam tool characterized the physiochemical parameters of the vaccine. At the same time, SOLpro evaluated our vaccine constructs to be soluble upon expression. We also modeled the stable tertiary structure of our vaccine construct through Robetta modeling for molecular docking studies with toll-like receptor proteins through HADDOCK 2.4. Simulations based on molecular dynamics revealed an intact vaccine and TLR8 complex, supporting our vaccine design's immunogenicity. Also, the immune simulation of our vaccine by the C-ImmSim server demonstrated the potency of the multiepitope vaccine construct to induce proper immune response for host defense. Codon optimization and in silico cloning of our vaccine further assured high expression. The outcomes of our study on multiepitope vaccine design significantly produced a potential candidate against VL and can potentially eradicate the disease in the future after clinical investigations.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Deep Bhowmik
- Deparment of Microbiology, Assam University, Silchar, Assam, India
| | - Achyut Bhuyan
- Deparment of Microbiology, Assam University, Silchar, Assam, India
| | - Seshan Gunalan
- Biopolymer Modelling Laboratory, Centre of Advanced Study in Crystallography and Biophysics, Guindy Campus, University of Madras, Chennai, India
| | - Gugan Kothandan
- Biopolymer Modelling Laboratory, Centre of Advanced Study in Crystallography and Biophysics, Guindy Campus, University of Madras, Chennai, India
| | - Diwakar Kumar
- Deparment of Microbiology, Assam University, Silchar, Assam, India
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Linani A, Serseg T, Benarous K, Bou-Salah L, Yousfi M, Alama MN, Ashraf GM. Cupressus sempervirens L. flavonoids as potent inhibitors to xanthine oxidase: in vitro, molecular docking, ADMET and PASS studies. J Biomol Struct Dyn 2023; 41:7055-7068. [PMID: 36001586 DOI: 10.1080/07391102.2022.2114943] [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: 04/11/2022] [Accepted: 08/14/2022] [Indexed: 10/15/2022]
Abstract
Excessive intake of purine-rich foods such as seafood and red meat leads to excess xanthine oxidase activity and provokes gout attacks. The aim of this paper is to evaluate in vitro and in silico, the inhibition effect of Cupressus sempervirens plant extracts (flavonoids (Cae) and alkaloids (CaK)) and its six derivative compounds on bovine xanthine oxidase (BXO). The in silico study consists of molecular docking with GOLD v4.0 based on the best PLPchem score (PLP) and prediction of biological activity with the PASS server tool. The inhibitors used were lignan (cp1), Amentoflavone (cp2), Cupressuflavone (cp3), Isocryptomerin (cp4), Hinokiflavone (cp5), and Neolignan (cp6). The in vitro results showed that CaK gives an IC50 of 3.52 ± 0.04 μg/ml. Similarly, Cae saved an IC50 of 8.46 ± 1.98 μg/ml compared with the control (2.82 ± 0.10 μg/ml). The in silico results show that cp1 was the best inhibitor model (PLP of 88.09) with approved pharmacokinetics. These findings suggest that cp1 and cp2 may offer good alternatives for the treatment of hyperuricemia; cp3 was moderate, while the others (cp4 to cp6) were considered weak inhibitors according to their PLP.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Abderahmane Linani
- Fundamental sciences laboratory, Amar Telidji University, Laghouat, Algeria
| | - Talia Serseg
- Fundamental sciences laboratory, Amar Telidji University, Laghouat, Algeria
| | - Khedidja Benarous
- Fundamental sciences laboratory, Amar Telidji University, Laghouat, Algeria
- Biology department, Amar Telidji University, Laghouat, Algeria
| | - Leila Bou-Salah
- Fundamental sciences laboratory, Amar Telidji University, Laghouat, Algeria
| | - Mohamed Yousfi
- Fundamental sciences laboratory, Amar Telidji University, Laghouat, Algeria
| | - Mohammed Nabil Alama
- Department of Cardiology, Faculty of Medicine, King Abdulaziz University Hospital, Jeddah, Saudi Arabia
| | - Ghulam Md Ashraf
- Pre-Clinical Research Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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Tian X, Xu J, Ye Y, Xiao X, Yan L, Yu S, Cai4 J, Du Q, Dong X, Zhou L, Shan L, Yuan Q. Gallic acid in theabrownin suppresses cell proliferation and migration in non‑small cell lung carcinoma via autophagy inhibition. Oncol Lett 2023; 26:294. [PMID: 37274480 PMCID: PMC10236267 DOI: 10.3892/ol.2023.13880] [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: 08/24/2022] [Accepted: 03/17/2023] [Indexed: 06/06/2023] Open
Abstract
The bioactive extract of green tea, theabrownin (TB), is known to exhibit pro-apoptotic and antitumor effects on non-small cell lung cancer (NSCLC). Gallic acid (GA) is a crucial component of TB; however, its mechanism of action in NSCLC has been rarely studied. To date, little attention has been paid to the anti-NSCLC activity of GA. Therefore, the present study investigated the effects of GA in vivo and in vitro. Cell Counting Kit (CCK)-8 assay, DAPI staining and flow cytometry, wound-healing assay and western blotting were used to assess cell viability, apoptosis, migration and protein expression, respectively. In addition, a xenograft model was generated, and TUNEL assay and immunohistochemistry analysis were performed. The CCK-8 data showed that the viability of H1299 cells was significantly inhibited by GA in a dose- and time-dependent manner. DAPI staining, Annexin-V/PI staining and wound-healing data showed that GA exerted pro-apoptotic and anti-migratory effects on H1299 cells in a dose-dependent manner. Furthermore, the results of western blotting showed that GA significantly upregulated the levels of pro-apoptotic proteins [cleaved (c-)PARP, c-caspase8, c-caspase-9 and the ratio of γ-H2A.X/H2A.X]. In vivo data confirmed the antitumor effect of GA through apoptosis induction in an autophagy-dependent manner. In conclusion, the present study confirmed the anti-proliferative, pro-apoptotic and anti-migratory effects of GA against NSCLC in vitro and in vivo, providing considerable evidence for its potential as a novel candidate for the treatment of NSCLC.
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Affiliation(s)
- Xue Tian
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, P.R. China
- The First Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, P.R. China
| | - Jiaan Xu
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, P.R. China
- The First Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, P.R. China
| | - Yonghua Ye
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, P.R. China
- The First Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, P.R. China
| | - Xiujuan Xiao
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, P.R. China
- The First Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, P.R. China
| | - Li Yan
- Cell Resource Bank and Integrated Cell Preparation Center of Xiaoshan District, Hangzhou Regional Cell Preparation Center (Shangyu Biotechnology Co., Ltd.), Hangzhou, Zhejiang 311200, P.R. China
| | - Shihui Yu
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, P.R. China
- The First Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, P.R. China
| | - Jianyong Cai4
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, P.R. China
| | - Quan Du
- Department of Neurosurgery, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, P.R. China
| | - Xiaoqiao Dong
- Department of Neurosurgery, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, P.R. China
| | - Li Zhou
- The First Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, P.R. China
- Cell Resource Bank and Integrated Cell Preparation Center of Xiaoshan District, Hangzhou Regional Cell Preparation Center (Shangyu Biotechnology Co., Ltd.), Hangzhou, Zhejiang 311200, P.R. China
| | - Letian Shan
- The First Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, P.R. China
- Cell Resource Bank and Integrated Cell Preparation Center of Xiaoshan District, Hangzhou Regional Cell Preparation Center (Shangyu Biotechnology Co., Ltd.), Hangzhou, Zhejiang 311200, P.R. China
| | - Qiang Yuan
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, P.R. China
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Rahman MN, Ahmed S, Hasan M, Shuvo MSA, Islam MA, Hasan R, Roy S, Hossain H, Mia MM. Immunoselective progression of a multi-epitope-based subunit vaccine candidate to convey protection against the parasite Onchocerca lupi. INFORMATICS IN MEDICINE UNLOCKED 2023. [DOI: 10.1016/j.imu.2023.101209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
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Sarkar B, Ullah MA, Araf Y, Islam NN, Zohora US. Immunoinformatics-guided designing and in silico analysis of epitope-based polyvalent vaccines against multiple strains of human coronavirus (HCoV). Expert Rev Vaccines 2022; 21:1851-1871. [PMID: 33435759 PMCID: PMC7989953 DOI: 10.1080/14760584.2021.1874925] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 01/08/2021] [Indexed: 01/12/2023]
Abstract
OBJECTIVES The group of human coronaviruses (HCoVs) consists of some highly pathogenic viruses that have caused several outbreaks in the past. The newly emerged strain of HCoV, the SARS-CoV-2 is responsible for the recent global pandemic that has already caused the death of hundreds of thousands of people due to the lack of effective therapeutic options. METHODS In this study, immunoinformatics methods were used to design epitope-based polyvalent vaccines which are expected to be effective against four different pathogenic strains of HCoV i.e., HCoV-OC43, HCoV-SARS, HCoV-MERS, and SARS-CoV-2. RESULTS The constructed vaccines consist of highly antigenic, non-allergenic, nontoxic, conserved, and non-homologous T-cell and B-cell epitopes from all the four viral strains. Therefore, they should be able to provide strong protection against all these strains. Protein-protein docking was performed to predict the best vaccine construct. Later, the MD simulation and immune simulation of the best vaccine construct also predicted satisfactory results. Finally, in silico cloning was performed to develop a mass production strategy of the vaccine. CONCLUSION If satisfactory results are achieved in further in vivo and in vitro studies, then the vaccines designed in this study might be effective as preventative measures against the selected HCoV strains.
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Affiliation(s)
- Bishajit Sarkar
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Md. Asad Ullah
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Yusha Araf
- Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Nafisa Nawal Islam
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Umme Salma Zohora
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Jahangirnagar University, Savar, Dhaka, Bangladesh
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Yousaf M, Ismail S, Ullah A, Bibi S. Immuno-informatics profiling of monkeypox virus cell surface binding protein for designing a next generation multi-valent peptide-based vaccine. Front Immunol 2022; 13:1035924. [PMID: 36405737 PMCID: PMC9668073 DOI: 10.3389/fimmu.2022.1035924] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 10/12/2022] [Indexed: 11/07/2022] Open
Abstract
Monkeypox is a viral etiological agent with hallmarks analogous to those observed in smallpox cases in the past. The ongoing outbreak of Monkeypox viral infection is becoming a global health problem. Multi-valent peptide based next generation vaccines provides us a promising solution to combat these emerging infectious diseases by eliciting cell-mediated and humoral immune response. Considering the success rate of subtractive proteomics pipeline and reverse vaccinology approach, in this study, we have developed a novel, next-generation, multi-valent, in silico peptide based vaccine construct by employing cell surface binding protein. After analyzing physiochemical and biological properties of the selected target, the protein was subjected to B cell derived T cell epitope mapping. Iterative scrutinization lead to the identification of two highly antigenic, virulent, non-allergic, non-toxic, water soluble, and Interferon-gamma inducer epitopes i.e. HYITENYRN and TTSPVRENY. We estimated that the shortlisted epitopes for vaccine construction, roughly correspond to 99.74% of the world’s population. UK, Finland and Sweden had the highest overall population coverage at 100% which is followed by Austria (99.99%), Germany (99.99%), France (99.98%), Poland (99.96), Croatia (99.93), Czech Republic (99.87%), Belgium (99.87), Italy (99.86%), China (97.83%), India (97.35%) and Pakistan (97.13%). The designed vaccine construct comprises of 150 amino acids with a molecular weight of 16.97242 kDa. Molecular docking studies of the modelled MEMPV (Multi-epitope Monkeypox Vaccine) with MHC I (PDB ID: 1I1Y), MHC II (PDB ID: 1KG0), and other immune mediators i.e. toll like receptors TLR3 (PDB ID: 2A0Z), and TLR4 (PDB ID: 4G8A) revealed strong binding affinity with immune receptors. Host immune simulation results predicted that the designed vaccine has strong potency to induce immune responses against target pathogen in the form of cellular and antibody-dependent immunity. Our findings suggest that the hypothesized vaccine candidate can be utilized as a potential therapeutic against Monkeypox however experimental study is required to validate the results and safe immunogenicity.
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Affiliation(s)
- Maha Yousaf
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
- *Correspondence: Maha Yousaf, ; Shabana Bibi,
| | - Saba Ismail
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Asad Ullah
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
| | - Shabana Bibi
- Department of Biosciences, Shifa Tameer-e-Millat University, Islamabad, Pakistan
- Yunnan Herbal Laboratory, College of Ecology and Environmental Sciences, Yunnan University, Kunming, China
- *Correspondence: Maha Yousaf, ; Shabana Bibi,
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Islam SI, Sanjida S, Ahmed SS, Almehmadi M, Allahyani M, Aljuaid A, Alsaiari AA, Halawi M. Core Proteomics and Immunoinformatic Approaches to Design a Multiepitope Reverse Vaccine Candidate against Chagas Disease. Vaccines (Basel) 2022; 10:vaccines10101669. [PMID: 36298534 PMCID: PMC9607777 DOI: 10.3390/vaccines10101669] [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: 09/06/2022] [Revised: 09/23/2022] [Accepted: 10/02/2022] [Indexed: 11/05/2022] Open
Abstract
Chagas disease is a tropical ailment indigenous to South America and caused by the protozoan parasite Trypanosoma cruzi, which has serious health consequences globally. Insect vectors transmit the parasite and, due to the lack of vaccine availability and limited treatment options, we implemented an integrated core proteomics analysis to design a reverse vaccine candidate based on immune epitopes for disease control. Firstly, T. cruzi core proteomics was used to identify immunodominant epitopes. Therefore, we designed the vaccine sequence to be non-allergic, antigenic, immunogenic, and to have better solubility. After predicting the tertiary structure, docking and molecular dynamics simulation (MDS) were performed with TLR4, MHC-I, and MHC-II receptors to discover the binding affinities. The final vaccine design demonstrated significant hydrogen bond interactions upon docking with TLR4, MHC-I, and MHC-II receptors. This indicated the efficacy of the vaccine candidate. A server-based immune simulation approach was generated to predict the efficacy. Significant structural compactness and binding stability were found based on MDS. Finally, by optimizing codons on Escherichia coli K12, a high GC content and CAI value were obtained, which were then incorporated into the cloning vector pET2+ (a). Thus, the developed vaccine sequence may be a viable therapy option for Chagas disease.
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Affiliation(s)
- Sk Injamamul Islam
- The International Graduate Program of Veterinary Science and Technology (VST), Department of Veterinary Microbiology, Faculty of Veterinary Science and Technology, Chulalongkorn University, Bangkok 10330, Thailand
- Correspondence: or
| | - Saloa Sanjida
- Department of Environmental Science and Technology, Faculty of Applied Science and Technology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Sheikh Sunzid Ahmed
- Department of Botany, Faculty of Biological Sciences, University of Dhaka, Dhaka 1000, Bangladesh
| | - Mazen Almehmadi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia
| | - Mamdouh Allahyani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia
| | - Abdulelah Aljuaid
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia
| | - Ahad Amer Alsaiari
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia
| | - Mustafa Halawi
- Department of Medical Laboratory Technology, College of Applied Medical Sciences, Jazan University, Jazan 54943, Saudi Arabia
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Mia MM, Hasan M, Ahmed S, Rahman MN. Insight into the first multi-epitope-based peptide subunit vaccine against avian influenza A virus (H5N6): An immunoinformatics approach. INFECTION, GENETICS AND EVOLUTION 2022; 104:105355. [PMID: 36007760 PMCID: PMC9394107 DOI: 10.1016/j.meegid.2022.105355] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 05/22/2022] [Accepted: 08/18/2022] [Indexed: 11/26/2022]
Abstract
The rampant spread of highly pathogenic avian influenza A (H5N6) virus has drawn additional concerns along with ongoing Covid-19 pandemic. Due to its migration-related diffusion, the situation is deteriorating. Without an existing effective therapy and vaccines, it will be baffling to take control measures. In this regard, we propose a revers vaccinology approach for prediction and design of a multi-epitope peptide based vaccine. The induction of humoral and cell-mediated immunity seems to be the paramount concern for a peptide vaccine candidate; thus, antigenic B and T cell epitopes were screened from the surface, membrane and envelope proteins of the avian influenza A (H5N6) virus, and passed through several immunological filters to determine the best possible one. Following that, the selected antigenic with immunogenic epitopes and adjuvant were linked to finalize the multi-epitope-based peptide vaccine by appropriate linkers. For the prediction of an effective binding, molecular docking was carried out between the vaccine and immunological receptors (TLR8). Strong binding affinity and good docking scores clarified the stringency of the vaccines. Furthermore, molecular dynamics simulation was performed within the highest binding affinity complex to observe the stability, and minimize the designed vaccine's high mobility region to order to increase its stability. Then, Codon optimization and other physicochemical properties were performed to reveal that the vaccine would be suitable for a higher expression at cloning level and satisfactory thermostability condition. In conclusion, predicting the overall in silico assessment, we anticipated that our designed vaccine would be a plausible prevention against avian influenza A (H5N6) virus.
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Affiliation(s)
- Md Mukthar Mia
- Department of Poultry Science, Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet 3100, Bangladesh; Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Mahamudul Hasan
- Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet 3100, Bangladesh.
| | - Shakil Ahmed
- Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Mohammad Nahian Rahman
- Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet 3100, Bangladesh
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Hasan M, Mia M. Exploratory Algorithm of a Multi-epitope-based Subunit Vaccine Candidate Against Cryptosporidium hominis: Reverse Vaccinology-Based Immunoinformatic Approach. Int J Pept Res Ther 2022; 28:134. [PMID: 35911179 PMCID: PMC9315849 DOI: 10.1007/s10989-022-10438-6] [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] [Accepted: 06/26/2022] [Indexed: 12/03/2022]
Abstract
Cryptosporidiosis is the leading protozoan-induced cause of diarrheal illness in children, and it has been linked to childhood mortality, malnutrition, cognitive development, with retardation of growth. Cryptosporidium hominis, the anthroponotically transmitted species within the Cryptosporidium genus, contributes significantly to the global burden of infection, accounting for the majority of clinical cases in numerous nations, as well as its emergence in the last decade is largely due to detections obtained through noteworthy epidemiologic research. Nevertheless, there is no vaccine available, and the only licensed medication, nitazoxanide, has been demonstrated to have efficacy limitations in a number of patient groups recognized to be at high risk of complications. Therefore, current study delineates the computational vaccine design for Cryptosporidium hominis, the notable pathogen for enteric diarrhea. Firstly, a comprehensive literature search was conducted to identify six proteins based on their toxigenicity, allergenicity, antigenicity, and prediction of transmembrane helices to make up a multi-epitope-based subunit vaccine. Following that, antigenic non-toxic HTL epitope, CTL epitope with B cell epitope were predicted from the selected proteins and construct a vaccine candidate with adding an adjuvant and some linkers with immunologically superior epitopes. Afterwards, the constructed vaccine candidates and TLR2 receptor were put into the ClusPro server for molecular dynamic simulation to know the binding stability of the vaccine-TLR2 complex. Following that, Escherichia coli strain K12 was used as a cloning host for the chosen vaccine construct via the JCat server. As a result of the findings, it was resolute that the proposed chimeric peptide vaccine could improve the immune response to Cryptosporidium hominis.
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Affiliation(s)
- Mahamudul Hasan
- Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet, 3100 Bangladesh
| | - Mukthar Mia
- Department of Poultry Science, Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet, 3100 Bangladesh.,Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet, 3100 Bangladesh
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Soltan MA, Behairy MY, Abdelkader MS, Albogami S, Fayad E, Eid RA, Darwish KM, Elhady SS, Lotfy AM, Alaa Eldeen M. In silico Designing of an Epitope-Based Vaccine Against Common E. coli Pathotypes. Front Med (Lausanne) 2022; 9:829467. [PMID: 35308494 PMCID: PMC8931290 DOI: 10.3389/fmed.2022.829467] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 01/21/2022] [Indexed: 12/20/2022] Open
Abstract
Escherichia coli (E. coli) is a Gram-negative bacterium that belongs to the family Enterobacteriaceae. While E. coli can stay as an innocuous resident in the digestive tract, it can cause a group of symptoms ranging from diarrhea to live threatening complications. Due to the increased rate of antibiotic resistance worldwide, the development of an effective vaccine against E. coli pathotypes is a major health priority. In this study, a reverse vaccinology approach along with immunoinformatics has been applied for the detection of potential antigens to develop an effective vaccine. Based on our screening of 5,155 proteins, we identified lipopolysaccharide assembly protein (LptD) and outer membrane protein assembly factor (BamA) as vaccine candidates for the current study. The conservancy of these proteins in the main E. coli pathotypes was assessed through BLASTp to make sure that the designed vaccine will be protective against major E. coli pathotypes. The multitope vaccine was constructed using cytotoxic T lymphocyte (CTL), helper T lymphocyte (HTL), and B cell lymphocyte (BCL) epitopes with suitable linkers and adjuvant. Following that, it was analyzed computationally where it was found to be antigenic, soluble, stable, and non-allergen. Additionally, the adopted docking study, as well as all-atom molecular dynamics simulation, illustrated the promising predicted affinity and free binding energy of this constructed vaccine against the human Toll-like receptor-4 (hTLR-4) dimeric state. In this regard, wet lab studies are required to prove the efficacy of the potential vaccine construct that demonstrated promising results through computational validation.
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Affiliation(s)
- Mohamed A. Soltan
- Department of Microbiology and Immunology, Faculty of Pharmacy, Sinai University, Ismailia, Egypt
| | - Mohammed Y. Behairy
- Department of Microbiology and Immunology, Faculty of Pharmacy, University of Sadat City, Sadat City, Egypt
| | - Mennatallah S. Abdelkader
- Department of Microbiology and Immunology, Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt
| | - Sarah Albogami
- Department of Biotechnology, College of Science, Taif University, Taif, Saudi Arabia
| | - Eman Fayad
- Department of Biotechnology, College of Science, Taif University, Taif, Saudi Arabia
| | - Refaat A. Eid
- Department of Pathology, College of Medicine, King Khalid University, Abha, Saudi Arabia
| | - Khaled M. Darwish
- Department of Medicinal Chemistry, Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt
| | - Sameh S. Elhady
- Department of Natural Products, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed M. Lotfy
- Department of Pharmacology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Muhammad Alaa Eldeen
- Division of Cell Biology, Histology and Genetics, Department of Zoology, Faculty of Science, Zagazig University, Zagazig, Egypt
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Design of a Novel Recombinant Multi-Epitope Vaccine against Triple-Negative Breast Cancer. IRANIAN BIOMEDICAL JOURNAL 2022; 26:160-74. [PMID: 35090304 PMCID: PMC8987416 DOI: 10.52547/ibj.26.2.160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Background Triple-negative breast cancer (TNBC) is determined by the absence of ERBB2, estrogen and progesterone receptors’ expression. Cancer vaccines, as the novel immunotherapy strategies, have emerged as promising tools for treating the advanced stage of TNBC. The aim of this study was to evaluate Carcinoembryonic antigen (CEA), Metadherin (MTDH), and Mucin 1 (MUC-1) proteins as vaccine candidates against TNBC. Methods In this research, a novel vaccine was designed against TNBC by using different immunoinformatics and bioinformatics approaches. Effective immunodominant epitopes were chosen from three antigenic proteins, namely CEA, MTDH, and MUC-1. Recombinant TLR4 agonists were utilized as an adjuvant to stimulate immune responses. Following the selection of antigens and adjuvants, appropriate linkers were chosen to generate the final recombinant protein. To achieve an excellent 3D model, the best predicted 3D model was required to be refined and validated. To demonstrate whether the vaccine/TLR4 complex is stable or not, we performed docking analysis and dynamic molecular simulation. Result Immunoinformatics and bioinformatics evaluations of the designed construct demonstrated that this vaccine candidate could effectively be used as a therapeutic armament against TNBC. Conclusion Bioinformatics studies revealed that the designed vaccine has an acceptable quality. Investigating the effectiveness of this vaccine can be confirmed by supplementary in vitro and in vivo studies.
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Rouzbahani AK, Kheirandish F, Hosseini SZ. Design of a multi-epitope-based peptide vaccine against the S and N proteins of SARS-COV-2 using immunoinformatics approach. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2022; 23:16. [PMID: 37521850 PMCID: PMC8813187 DOI: 10.1186/s43042-022-00224-w] [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: 07/15/2021] [Accepted: 11/13/2021] [Indexed: 11/10/2022] Open
Abstract
Background As the new pandemic created by COVID-19 virus created the need of rapid acquisition of a suitable vaccine against SARS-CoV-2 to develop Immunity and to reduce the mortality, the aim of this study was to identify SARS-CoV-2 S protein and N antigenic epitopes by using immunoinformatic methods to design a vaccine against SARS-CoV-2, for which S and N protein-dependent epitopes are predicted. B cell, CTL and HTL were determined based on antigenicity, allergenicity and toxicity that were non-allergenic, non-toxic, and antigenic and were selected for the design of a multi-epitope vaccine structure. Then, in order to increase the safety of Hbd-3 and Hbd-2 as adjuvants, they were connected to the N and C terminals of the vaccine construct, respectively, with a linker. The three-dimensional structure of the structure was predicted and optimized, and its quality was evaluated. The vaccine construct was ligated to MHCI. Finally, after optimizing the codon to increase expression in E. coli K12, the vaccine construct was cloned into pET28a (+) vector. Results Epitopes which were used in our survey were based on non-allergenic, non-toxic and antigenic. Therefore, 543-amino-acid-long multi-epitope vaccine formation was invented through linking 9 cytotoxic CTL, 5 HTL and 14 B cell epitopes with appropriate adjuvants and connectors that can control the SARS coronavirus 2 infection and could be more assessed in medical scientific researches. Conclusion We believe that the proposed multi-epitope vaccine can effectively evoke an immune response toward SARS-CoV-2. Supplementary Information The online version contains supplementary material available at 10.1186/s43042-022-00224-w.
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Affiliation(s)
| | - Farnaz Kheirandish
- Department of Medical Parasitology and Mycology, School of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran
- Department of Medical Biotechnology, School of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Seyedeh Zeinab Hosseini
- Razi Herbal Medicines Research Center, Lorestan University of Medical Sciences, Khorramabad, Iran
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Banik A, Ahmed SR, Marma H, Sinha S, Rahman Khan MM, Miah K. Targeting mucormycosis polyprotein (RVT_1 region) through antifungal phytochemicals of plants: An in-silico perspective. INFORMATICS IN MEDICINE UNLOCKED 2022. [DOI: 10.1016/j.imu.2022.100851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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15
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Mia MM, Hasan M, Hasan MM, Khan SS, Rahman MN, Ahmed S, Basak A, Sakib MN, Banik S. Multi-epitope based subunit vaccine construction against Banna virus targeting on two outer proteins (VP4 and VP9): A computational approach. INFECTION GENETICS AND EVOLUTION 2021; 95:105076. [PMID: 34500093 DOI: 10.1016/j.meegid.2021.105076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 08/28/2021] [Accepted: 09/03/2021] [Indexed: 11/17/2022]
Abstract
Recently, RNA viruses have gained a mammoth concern for causing various outbreaks, and due to pandemics, they are acquiring additional attention throughout the world. An emerging RNA as well as vector-borne Banna Virus (BAV) is a human pathogen resulting in encephalitis, fever, headache, muscle aches, and severe coma. Besides human, pathogenic BAV was also detected from pigs, cattle, ticks, midges, and mosquitoes in Indonesia, China, and Vietnam. Due to high mutation tendency and dearth of a species barrier, this virus will consider as a significant threat in the near future throughout the planet, particularly in Africa. Despite of severe human case fatalities in several countries, there are no specific therapeutics, available vaccines, and other preventive measures against BAV. Thus, to find out the effective therapeutics and preventive strategies are crying exigency. In the present study, a unique multi-epitope-based peptide vaccine candidate is constructed using bioinformatics' tools that efficiently instigate immune cells for generating BAV antibodies. The potential vaccine candidates were developed using both T and B -cell epitopes. UniprotKB database was used to retrieve of two outer proteins (VP9 and VP4), and homologous sequences of BAV taxid: 7763, 649,604, 77,763, and 8453 were searched by NCBI BLAST. These serotypes are the most closely associated with the disease. Then combining the best-selected epitopes in various combinations with different adjuvants, three distinct vaccine candidates were formed. The validity tests were performed for the screened vaccine candidate regarding stability, allergenicity, and antigenicity parameters. Moreover, molecular dynamic simulations of the selected vaccine with TLR-8 immune receptor confirmed the stability of the binding pose and showed a significant response to immune cells. Thus, the results established that the designed chimeric peptide vaccine could enhance the immune response against BAV.
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Affiliation(s)
- Md Mukthar Mia
- Department of Poultry Science, Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet 3100, Bangladesh; Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet 3100, Bangladesh..
| | - Mahamudul Hasan
- Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet 3100, Bangladesh..
| | - Md Mahadi Hasan
- Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Sumaya Shargin Khan
- Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Mohammad Nahian Rahman
- Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Shakil Ahmed
- Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Ankita Basak
- Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Md Nazmuj Sakib
- Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Shrabonti Banik
- Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet 3100, Bangladesh
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In Silico Prediction of a Multitope Vaccine against Moraxella catarrhalis: Reverse Vaccinology and Immunoinformatics. Vaccines (Basel) 2021; 9:vaccines9060669. [PMID: 34207238 PMCID: PMC8234879 DOI: 10.3390/vaccines9060669] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 05/25/2021] [Accepted: 06/01/2021] [Indexed: 02/05/2023] Open
Abstract
Moraxella catarrhalis (M. catarrhalis) is a Gram-negative bacterium that can cause serious respiratory tract infections and middle ear infections in children and adults. M. catarrhalis has demonstrated an increasing rate of antibiotic resistance in the last few years, thus development of an effective vaccine is a major health priority. We report here a novel designed multitope vaccine based on the mapped epitopes of the vaccine candidates filtered out of the whole proteome of M. catarrhalis. After analysis of 1615 proteins using a reverse vaccinology approach, only two proteins (outer membrane protein assembly factor BamA and LPS assembly protein LptD) were nominated as potential vaccine candidates. These proteins were found to be essential, outer membrane, virulent and non-human homologs with appropriate molecular weight and high antigenicity score. For each protein, cytotoxic T lymphocyte (CTL), helper T lymphocyte (HTL) and B cell lymphocyte (BCL) epitopes were predicted and confirmed to be highly antigenic and cover conserved regions of the proteins. The mapped epitopes constituted the base of the designed multitope vaccine where suitable linkers were added to conjugate them. Additionally, beta defensin adjuvant and pan-HLA DR-binding epitope (PADRE) peptide were also incorporated into the construct to improve the stimulated immune response. The constructed multitope vaccine was analyzed for its physicochemical, structural and immunological characteristics and it was found to be antigenic, soluble, stable, non-allergenic and have a high affinity to its target receptor. Although the in silico analysis of the current study revealed that the designed multitope vaccine has the ability to trigger a specific immune response against M. catarrhalis, additional translational research is required to confirm the effectiveness of the designed vaccine.
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17
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Abdelli I, Hassani F, Bekkel Brikci S, Ghalem S. In silico study the inhibition of angiotensin converting enzyme 2 receptor of COVID-19 by Ammoides verticillata components harvested from Western Algeria. J Biomol Struct Dyn 2021; 39:3263-3276. [PMID: 32362217 PMCID: PMC7232889 DOI: 10.1080/07391102.2020.1763199] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 04/24/2020] [Indexed: 12/20/2022]
Abstract
The objective of this present study is to focus on the in silico study to screen for an alternative drug that can block the activity of the angiotensin converting enzyme 2 (ACE2) as a receptor for SARS-CoV-2, potential therapeutic target of the COVID-19 virus using natural compounds (Isothymol, Thymol, Limonene, P-cymene and γ-terpinene) derived from the essential oil of the antiviral and antimicrobial plant Ammoides verticillata (Desf.) Briq. which is located in the occidental Algeria areas. This study reveals that Isothymol, a major component of this plant, gives the best docking scores, compared to, the co-crystallized inhibitor β-D-mannose of the enzyme ACE2, to Captropil drug as good ACE2 inhibitor and to Chloroquine antiviral drug also involved in other mechanisms as inhibition of ACE2 cellular receptor. In silico (ADME), drug-likeness, PASS & P450 site of metabolism prediction, pharmacophore Mapper showed that the compound Isothymol has given a good tests results compared to the β-D-mannose co-crystallized inhibitor, to Captopril and Chloroquine drugs. Also the other natural compounds gave good results. The Molecular Dynamics Simulation study showed good result for the Isotymol- ACE2 docked complex. This study revealed for the first time that Isothymol is a functional inhibitor of angiotensin converting enzyme 2 activity and the components of essential oils Ammoides verticillata can be used as potential inhibitors to the ACE2 receptor of SARS-CoV-2.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Imane Abdelli
- Higher School of Applied Sciences, Tlemcen, Algeria
- Laboratory of Natural and bio-actives Substances, Faculty of Science- University, Tlemcen, Algeria
| | - Faiçal Hassani
- Ecology and Management of Naturals Ecosystems Laboratory, Department of Ecology and Environment, Faculty SNV-STU- University, Tlemcen, Algeria
| | - Sohayb Bekkel Brikci
- Ecology and Management of Naturals Ecosystems Laboratory, Department of Ecology and Environment, Faculty SNV-STU- University, Tlemcen, Algeria
| | - Said Ghalem
- Laboratory of Natural and bio-actives Substances, Faculty of Science- University, Tlemcen, Algeria
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18
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Azim KF, Lasker T, Akter R, Hia MM, Bhuiyan OF, Hasan M, Hossain MN. Combination of highly antigenic nucleoproteins to inaugurate a cross-reactive next generation vaccine candidate against Arenaviridae family. Heliyon 2021; 7:e07022. [PMID: 34041391 PMCID: PMC8144012 DOI: 10.1016/j.heliyon.2021.e07022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 02/09/2021] [Accepted: 05/05/2021] [Indexed: 12/28/2022] Open
Abstract
Arenaviral infections often result lethal hemorrhagic fevers, affecting primarily in African and South American regions. To date, there is no FDA-approved licensed vaccine against arenaviruses and treatments have been limited to supportive therapy. Hence, the study was employed to design a highly immunogenic cross-reactive vaccine against Arenaviridae family using reverse vaccinology approach. The whole proteome of Lassa virus (LASV), Lymphocytic Choriomeningitis virus (LCMV), Lujo virus and Guanarito virus were retrieved and assessed to determine the most antigenic viral proteins. Both T-cell and B-cell epitopes were predicted and screened based on transmembrane topology, antigenicity, allergenicity, toxicity and molecular docking analysis. The final constructs were designed using different adjuvants, top epitopes, PADRE sequence and respective linkers and were assessed for the efficacy, safety, stability and molecular cloning purposes. The proposed epitopes were highly conserved (84%–100%) and showed greater cumulative population coverage. Moreover, T cell epitope GWPYIGSRS was conserved in Junin virus (Argentine mammarenavirus) and Sabia virus (Brazilian mammarenavirus), while B cell epitope NLLYKICLSG was conserved in Machupo virus (Bolivian mammarenavirus) and Sabia virus, indicating the possibility of final vaccine construct to confer a broad range immunity in the host. Docking analysis of the refined vaccine with different MHC molecules and human immune receptors were biologically significant. The vaccine-receptor (V1-TLR3) complex showed minimal deformability at molecular level and was compatible for cloning into pET28a(+) vector of E. coli strain K12. The study could be helpful in developing vaccine to combat arenaviral infections in the future. However, further in vitro and in vivo trials using model animals are highly recommended for the experimental validation of our findings.
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Affiliation(s)
- Kazi Faizul Azim
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet 3100, Bangladesh.,Department of Microbial Biotechnology, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Tahera Lasker
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Rahima Akter
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Mantasha Mahmud Hia
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Omar Faruk Bhuiyan
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Mahmudul Hasan
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet 3100, Bangladesh.,Department of Pharmaceuticals and Industrial Biotechnology, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Md Nazmul Hossain
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet 3100, Bangladesh.,Department of Microbial Biotechnology, Sylhet Agricultural University, Sylhet 3100, Bangladesh
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Ahmed RA, Almofti YA, Abd-elrahman KA. Structural Analysis of the Polymerase Protein for Multiepitopes Vaccine Prediction against Hepatitis B Virus. BIOSCIENCES BIOTECHNOLOGY RESEARCH ASIA 2021; 18:125-146. [DOI: 10.13005/bbra/2902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Hepatitis B virus (HBV) is the most common cause of hepatocellular carcinoma and liver cirrhosis with significant morbidity and mortality worldwide. DNA polymerase protein of HBV is the immunogenic protein inducing immune response against B and T cells. The aim of this study wasto develop multi-epitope vaccine fromthe polymerase protein elicitingimmune responses.The predicted vaccine comprises epitopes against B and T lymphocytesobtained by IEDB server. The predicted epitopes were linked via suitable spacers (linkers). The 50S ribosomal protein L7/L12 was used as an adjuvant at amino terminal and His-tag at the carboxyl terminal of the vaccine construct. The candidate vaccine contains 457aa and was potentially antigenic and nonallergic. Vaccine molecular weightwas 50.03 KDa with pI of 10.04. The instability index was 25.78 and GRAVY was -0.354 indicating stability andhydrophilicity of the chimeric vaccine,respectively.Vaccine structure (Secondary and tertiary structures) were predicted, refined and used for molecular docking with TLR4.The docking with TLR4 provided energy scores of -1458.7 and -1410.3 for chain A and B, respectively, demonstrated strong binding between the chimeric vaccine and TLR4 chains.The vaccine provided favorable solubility compared to E. coli proteins. Stability via disulfide bonds engineering was predicted to reduce the entropy and mobility regions invaccine construct. Molecular dynamics simulation wasperformed to strengthen the prediction. In silicomolecular cloning was usedto guarantee the efficient clonabilityof the vaccine and translation within suitable vector.
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Affiliation(s)
- Rolla Abdalkader Ahmed
- Department of Microbiology, Faculty of laboratory science, Omdurman Ahlia University, Khartoum- Sudan
| | - Yassir A. Almofti
- Department of Molecular Biology and Bioinformatics, College of Veterinary Medicine, University of Bahri, Khartoum- Sudan
| | - Khoubieb Ali Abd-elrahman
- 3Department of pharmaceutical technology, College of Pharmacy, University of Medical Science and Technology (MUST) Khartoum- Sudan
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Mesli F, Ghalem M, Daoud I, Ghalem S. Potential inhibitors of angiotensin converting enzyme 2 receptor of COVID-19 by Corchorus olitorius Linn using docking, molecular dynamics, conceptual DFT investigation and pharmacophore mapping. J Biomol Struct Dyn 2021; 40:7311-7323. [PMID: 33706683 DOI: 10.1080/07391102.2021.1896389] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
A novel coronavirus, previously designated 2019-nCoV, was identified as the cause of a cluster of pneumonia cases in Wuhan, a city in the Hubei Province of China, at the end of 2019. Our objective focuses on the in silico study to screen for an alternative drug that can block the activity of the angiotensin converting enzyme 2 (ACE2), which is a key protein in the physiology of Covid-19, necessary for the entry of the SARS-Cov-2 virus into the host's cells using natural compounds especially phenolic antioxidants, polyphenolics and pharmaceutically phytochemicals derived from the leaves of Corchorus olitorius Linn, appear to be very potential in controlling virus-induced infection. The results of the docking simulation revealed that méthyl-1,4,5-tri-O-caféoyl quinate has a stronger bond, high affinity and gives the best docking scores compared to, the co-crystallized inhibitor (PRD_002214) of the enzyme ACE2, chloroquine, hydroxychloroquine, captopril and simerprevir antiviral drugs. The ADMET properties, Pharmacokinetics and Medicinal Chemistry & P450 site of metabolism prediction, pharmacophore Mapper enzyme revealed that the compound méthyl-1,4,5-tri-O-caféoyl quinate generates a hypothesis which can be applied successfully in biological screening for further experiments. The novel MD computational technique study showed better conformational movements result for the méthyl-1,4,5-tri-O-caféoyl quinate-ACE2 docked complex. Therefore méthyl-1,4,5-tri-O-caféoyl quinate may be considered to be potential inhibitor of the main protease enzyme of virus, but need to be investigated in vivo and in vitro for further drug development process.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Fouzia Mesli
- Department of Chemistry, Abu-Bakr Belkaid University of Tlemcen, Tlemcen, Algeria.,Laboratory of Naturals Products and Bioactive-Lasnabio, Tlemcen, Algeria
| | - Meriem Ghalem
- Department of Chemistry, Abu-Bakr Belkaid University of Tlemcen, Tlemcen, Algeria.,Department of Biology, Abu-Bakr Belkaid University of Tlemcen, Tlemcen, Algeria
| | - Ismail Daoud
- Laboratory of Naturals Products and Bioactive-Lasnabio, Tlemcen, Algeria.,Department of Matter Sciences, Mohamed Khider University of Biskra, Biskra, Algeria
| | - Said Ghalem
- Department of Chemistry, Abu-Bakr Belkaid University of Tlemcen, Tlemcen, Algeria.,Laboratory of Naturals Products and Bioactive-Lasnabio, Tlemcen, Algeria
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21
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Chenafa H, Mesli F, Daoud I, Achiri R, Ghalem S, Neghra A. In silico design of enzyme α-amylase and α-glucosidase inhibitors using molecular docking, molecular dynamic, conceptual DFT investigation and pharmacophore modelling. J Biomol Struct Dyn 2021; 40:6308-6329. [PMID: 33554773 DOI: 10.1080/07391102.2021.1882340] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Type 2 diabetes mellitus (T2DM) is characterized by elevated blood glucose levels and can lead to serious complications such as nephropathy, neuropathy, retinopathy and cardiovascular disease. The aim of this work is to identify and investigate the inhibition mechanism of natural flavonoids and phenolics acids against, the α-amylase (αA) and α-glucosidase (αG). Therefore, we used different approaches; such as conceptual DFT and pharmacophore mapping in addition to molecular mechanics, dynamics and docking simulations. Whereas, a close agreement was found out to decide that Linarin (Flavones) provides more optimized inhibition of αA and αG enzymes. Our results have shown that Linarin could be useful as preventative agent, and possibly therapeutic modality for the treatment of metabolic diseases.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hadjer Chenafa
- Laboratory of Therapeutic Chemistry, Annaba, Algeria.,Department of Pharmacy, Faculty of Medicine, BADJI Mokhtar University of Annaba, Annaba, Algeria
| | - Fouzia Mesli
- Department of Chemistry, Abu-Bakr Belk aid University of Tlemcen, Tlemcen, Algeria.,Laboratory of Naturals Products and Bioactive - Lasnabio, Tlemcen, Algeria
| | - Ismail Daoud
- Laboratory of Naturals Products and Bioactive - Lasnabio, Tlemcen, Algeria.,Department of Matter Sciences, Mohamed Khider University of Biskra, Biskra, Algeria
| | - Radja Achiri
- Department of Chemistry, Abu-Bakr Belk aid University of Tlemcen, Tlemcen, Algeria.,Laboratory of Naturals Products and Bioactive - Lasnabio, Tlemcen, Algeria
| | - Said Ghalem
- Department of Chemistry, Abu-Bakr Belk aid University of Tlemcen, Tlemcen, Algeria.,Laboratory of Naturals Products and Bioactive - Lasnabio, Tlemcen, Algeria
| | - Abdelhak Neghra
- Laboratory of Therapeutic Chemistry, Annaba, Algeria.,Department of Pharmacy, Faculty of Medicine, BADJI Mokhtar University of Annaba, Annaba, Algeria
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Akhand MRN, Azim KF, Hoque SF, Moli MA, Joy BD, Akter H, Afif IK, Ahmed N, Hasan M. Genome based evolutionary lineage of SARS-CoV-2 towards the development of novel chimeric vaccine. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2020; 85:104517. [PMID: 32882432 PMCID: PMC7462568 DOI: 10.1016/j.meegid.2020.104517] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/28/2020] [Accepted: 08/25/2020] [Indexed: 02/07/2023]
Abstract
The present study aimed to predict a novel chimeric vaccine by simultaneously targeting four major structural proteins via the establishment of ancestral relationship among different strains of coronaviruses. Conserved regions from the homologous protein sets of spike glycoprotein, membrane protein, envelope protein and nucleocapsid protein were identified through multiple sequence alignment. The phylogeny analyses of whole genome stated that four proteins reflected the close ancestral relation of SARS-CoV-2 to SARS-COV-1 and bat coronavirus. Numerous immunogenic epitopes (both T cell and B cell) were generated from the common fragments which were further ranked on the basis of antigenicity, transmembrane topology, conservancy level, toxicity and allergenicity pattern and population coverage analysis. Top putative epitopes were combined with appropriate adjuvants and linkers to construct a novel multiepitope subunit vaccine against COVID-19. The designed constructs were characterized based on physicochemical properties, allergenicity, antigenicity and solubility which revealed the superiority of construct V3 in terms safety and efficacy. Essential molecular dynamics and normal mode analysis confirmed minimal deformability of the refined model at molecular level. In addition, disulfide engineering was investigated to accelerate the stability of the protein. Molecular docking study ensured high binding affinity between construct V3 and HLA cells, as well as with different host receptors. Microbial expression and translational efficacy of the constructs were checked using pET28a(+) vector of E. coli strain K12. However, the in vivo and in vitro validation of suggested vaccine molecule might be ensured with wet lab trials using model animals for the implementation of the presented data.
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Affiliation(s)
- Mst Rubaiat Nazneen Akhand
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh,Department of Biochemistry and Chemistry, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | - Kazi Faizul Azim
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh,Department of Microbial Biotechnology, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | - Syeda Farjana Hoque
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh,Department of Pharmaceuticals and Industrial Biotechnology, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Mahmuda Akther Moli
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh,Department of Pharmaceuticals and Industrial Biotechnology, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Bijit Das Joy
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh,Department of Biochemistry and Chemistry, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | - Hafsa Akter
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | - Ibrahim Khalil Afif
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Nadim Ahmed
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | - Mahmudul Hasan
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh; Department of Pharmaceuticals and Industrial Biotechnology, Sylhet Agricultural University, Sylhet 3100, Bangladesh.
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Banik A, Ahmed SR, Sajib EH, Deb A, Sinha S, Azim KF. Identification of potential inhibitory analogs of metastasis tumor antigens (MTAs) using bioactive compounds: revealing therapeutic option to prevent malignancy.. [DOI: 10.1101/2020.10.19.345975] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
AbstractThe deeper understanding of metastasis phenomenon and detection of drug targets could be a potential approach to minimize cancer mortality. In this study, attempts were taken to unmask novel therapeutics to prevent metastasis and cancer progression. Initially, we explored the physiochemical, structural and functional insights of three metastasis tumor antigens (MTAs) and evaluated some plant based bioactive compounds as potent MTA inhibitors. From 50 plant metabolites screened, isoflavone, gingerol, citronellal and asiatic acid showed maximum binding affinity with all three MTA proteins. The ADME analysis detected no undesirable toxicity that could reduce the drug likeness properties of top plant metabolites. Moreover, molecular dynamics studies revealed that the complexes were stable and showed minimum fluctuation at molecular level. We further performed ligand based virtual screening to identify similar drug molecules using a large collection of 3,76,342 compounds from DrugBank. The results suggested that several structural analogs (e.g. Tramadol, Nabumetone, DGLA, Hydrocortisone) may act as agonist to block the MTA proteins and inhibit cancer progression at early stage. The study could be useful to develop effective medications against cancer metastasis in future. Due to encouraging results, we highly recommend furtherin vitroandin vivotrials for the experimental validation of the findings.
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Du J, Guo J, Kang D, Li Z, Wang G, Wu J, Zhang Z, Fang H, Hou X, Huang Z, Li G, Lu X, Liu X, Ouyang L, Rao L, Zhan P, Zhang X, Zhang Y. New techniques and strategies in drug discovery. CHINESE CHEM LETT 2020. [DOI: 10.1016/j.cclet.2020.03.028] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Ullah MA, Sarkar B, Islam SS. Exploiting the reverse vaccinology approach to design novel subunit vaccines against Ebola virus. Immunobiology 2020; 225:151949. [PMID: 32444135 DOI: 10.1016/j.imbio.2020.151949] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 03/19/2020] [Accepted: 04/20/2020] [Indexed: 01/17/2023]
Abstract
Ebola virus is a highly pathogenic RNA virus that causes the Ebola haemorrhagic fever in human. This virus is considered as one of the dangerous viruses in the world with very high mortality rate. To date, no epitope-based subunit vaccine has yet been discovered to fight against Ebola although the outbreaks of this deadly virus took many lives in the past. In this study, approaches of reverse vaccinology were utilized in combination with different tools of immunoinformatics to design subunit vaccines against Ebola virus strain Mayinga-76. Three potential antigenic proteins of this virus i.e., matrix protein VP40, envelope glycoprotein and nucleoprotein were selected to construct the subunit vaccine. The MHC class-I, MHC class-II and B-cell epitopes were determined initially and after some robust analysis i.e., antigenicity, allergenicity, toxicity, conservancy and molecular docking study, EV-1, EV-2 and EV-3 were constructed as three potential vaccine constructs. These vaccine constructs are also expected to be effective on few other strains of Ebola virus since the highly conserved epitopes were used for vaccine construction. Thereafter, molecular docking study was conducted on these vaccines and EV-1 emerged as the best vaccine construct. Afterward, molecular dynamics simulation study revealed the good performances and stability of the intended vaccine protein. Finally, codon adaptation and in silico cloning were carried out to design a possible plasmid (pET-19b plasmid vector was used) for large scale production of the EV-1 vaccine. However, further in vitro and in vivo studies might be required on the predicted vaccines for final validation.
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Affiliation(s)
- Md Asad Ullah
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Bishajit Sarkar
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Jahangirnagar University, Savar, Dhaka, Bangladesh.
| | - Syed Sajidul Islam
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Jahangirnagar University, Savar, Dhaka, Bangladesh
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26
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Thirumal Kumar D, Jain N, Udhaya Kumar S, George Priya Doss C, Zayed H. Identification of potential inhibitors against pathogenic missense mutations of PMM2 using a structure-based virtual screening approach. J Biomol Struct Dyn 2020; 39:171-187. [PMID: 31870226 DOI: 10.1080/07391102.2019.1708797] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The autosomal recessive phosphomannomutase 2-congenital disorder of glycosylation (PMM2-CDG) is characterized by defective functioning of the PMM2 enzyme, which is necessary for the conversion of mannose-6-phosphate into mannose-1-phosphate. Here, a computational pipeline was drawn to identify the most significant mutations, and further, we used a virtual screening approach to identify a new lead compound to treat the identified significant mutations. We searched for missense mutation data related to PMM2-CDG in HGMD®, UniProt, and ClinVar. Our search yielded a total of 103 mutations, of which 91 are missense mutations. The D65Y, I132N, I132T, and F183S mutations were classified as deleterious, destabilizing, and altering the biophysical properties using the PredictSNP, iStable, and Align GVGD in silico prediction tools. Additionally, we applied a multistep protocol to screen for an alternative lead compound to the existing CID2876053 (1-(3-chlorophenyl)-3,3-bis(pyridine-2-yl)urea) with affinity to these identified significant mutants. Two compounds, CHEMBL1491007 (6-chloro-4-phenyl-3-(4-pyridin-2-ylpiperazin-1-yl)-1H-quinolin-2-one) and CHEMBL3653029 (5-chloro-4-[6-[(3-fluorophenyl)methylamino]pyridin-2-yl]-N-(piperidin-4-ylmethyl)pyridin-2-amine), exhibited the highest binding affinity with the selected mutants and were chosen for further analysis. Through molecular docking, molecular dynamics simulation, and MMPBSA analysis, we found that the known compound, i.e. CID2876053, has stronger interaction with the D65Y mutant. The newly identified lead compound CHEMBL1491007 showed stronger interaction with the I132N and I132T mutants, whereas the most deleterious mutant, F183S, showed stronger interaction with CHEMBL3653029. This study is expected to aid in the field of precision medicine, and further to in vivo and in vitro analysis of these lead compounds might shed light on the treatment of PMM2-CDG. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- D Thirumal Kumar
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Nikita Jain
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, India
| | - S Udhaya Kumar
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, India
| | - C George Priya Doss
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health and Sciences, Qatar University, Doha, Qatar
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Dar HA, Waheed Y, Najmi MH, Ismail S, Hetta HF, Ali A, Muhammad K. Multiepitope Subunit Vaccine Design against COVID-19 Based on the Spike Protein of SARS-CoV-2: An In Silico Analysis. J Immunol Res 2020; 2020:8893483. [PMID: 33274246 PMCID: PMC7678744 DOI: 10.1155/2020/8893483] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/16/2020] [Accepted: 11/02/2020] [Indexed: 02/07/2023] Open
Abstract
The global health crisis caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causal agent of COVID-19, has resulted in a negative impact on human health and on social and economic activities worldwide. Researchers around the globe need to design and develop successful therapeutics as well as vaccines against the novel COVID-19 disease. In the present study, we conducted comprehensive computer-assisted analysis on the spike glycoprotein of SARS-CoV-2 in order to design a safe and potent multiepitope vaccine. In silico epitope prioritization shortlisted six HLA I epitopes and six B-cell-derived HLA II epitopes. These high-ranked epitopes were all connected to each other via flexible GPGPG linkers, and at the N-terminus side, the sequence of Cholera Toxin β subunit was attached via an EAAAK linker. Structural modeling of the vaccine was performed, and molecular docking analysis strongly suggested a positive association of a multiepitope vaccine with Toll-like Receptor 3. The structural investigations of the vaccine-TLR3 complex revealed the formation of fifteen interchain hydrogen bonds, thus validating its integrity and stability. Moreover, it was found that this interaction was thermodynamically feasible. In conclusion, our data supports the proposition that a multiepitope vaccine will provide protective immunity against COVID-19. However, further in vivo and in vitro experiments are needed to validate the immunogenicity and safety of the candidate vaccine.
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Affiliation(s)
- Hamza Arshad Dar
- 1Foundation University Medical College, Foundation University Islamabad, Islamabad 44000, Pakistan
| | - Yasir Waheed
- 1Foundation University Medical College, Foundation University Islamabad, Islamabad 44000, Pakistan
| | - Muzammil Hasan Najmi
- 1Foundation University Medical College, Foundation University Islamabad, Islamabad 44000, Pakistan
| | - Saba Ismail
- 1Foundation University Medical College, Foundation University Islamabad, Islamabad 44000, Pakistan
| | - Helal F. Hetta
- 2Department of Internal Medicine, University of Cincinnati College of Medicine, 231 Albert Sabin Way, Cincinnati, OH 45267-0595, USA
- 3Department of Medical Microbiology and Immunology, Faculty of Medicine, Assiut University, Assiut 71515, Egypt
| | - Amjad Ali
- 4Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad 44000, Pakistan
| | - Khalid Muhammad
- 5Department of Biology, College of Science, United Arab Emirates University, Al Ain 15551, UAE
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Sarkar B, Ullah MA, Araf Y. A systematic and reverse vaccinology approach to design novel subunit vaccines against Dengue virus type-1 (DENV-1) and human Papillomavirus-16 (HPV-16). INFORMATICS IN MEDICINE UNLOCKED 2020. [DOI: 10.1016/j.imu.2020.100343] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
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29
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Hasan M, Islam S, Chakraborty S, Mustafa AH, Azim KF, Joy ZF, Hossain MN, Foysal SH, Hasan MN. Contriving a chimeric polyvalent vaccine to prevent infections caused by herpes simplex virus (type-1 and type-2): an exploratory immunoinformatic approach. J Biomol Struct Dyn 2019; 38:2898-2915. [PMID: 31328668 DOI: 10.1080/07391102.2019.1647286] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Herpes simplex virus type 1 (HSV-1) and 2 (HSV-2) cause a variety of infections including oral-facial infections, genital herpes, herpes keratitis, cutaneous infection and so on. To date, FDA-approved licensed HSV vaccine is not available yet. Hence, the study was conducted to identify and characterize an effective epitope based polyvalent vaccine against both types of Herpes Simplex Virus. The selected proteins were retrieved from ViralZone and assessed to design highly antigenic epitopes by binding analyses of the peptides with MHC class-I and class-II molecules, antigenicity screening, transmembrane topology screening, allergenicity and toxicity assessment, population coverage analysis and molecular docking approach. The final vaccine was constructed by the combination of top CTL, HTL and BCL epitopes from each protein along with suitable adjuvant and linkers. Physicochemical and secondary structure analysis, disulfide engineering, molecular dynamic simulation and codon adaptation were further employed to develop a unique multi-epitope peptide vaccine. Docking analysis of the refined vaccine structure with different MHC molecules and human immune TLR-2 receptor demonstrated higher interaction. Complexed structure of the modeled vaccine and TLR-2 showed minimal deformability at molecular level. Moreover, translational potency and microbial expression of the modeled vaccine was analyzed with pET28a(+) vector for E. coli strain K12 and the vaccine constructs had no similarity with entire human proteome. The study enabled design of a novel chimeric polyvalent vaccine to confer broad range immunity against both HSV serotypes. However, further wet lab based research using model animals are highly recommended to experimentally validate our findings.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mahmudul Hasan
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, Bangladesh.,Department of Pharmaceuticals and Industrial Biotechnology, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Shiful Islam
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Sourav Chakraborty
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Abu Hasnat Mustafa
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Kazi Faizul Azim
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, Bangladesh.,Department of Microbial Biotechnology, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Ziaul Faruque Joy
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, Bangladesh.,Department of Biomedical Science, University of Sheffield, Sheffield, UK
| | - Md Nazmul Hossain
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, Bangladesh.,Department of Microbial Biotechnology, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Shakhawat Hossain Foysal
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Md Nazmul Hasan
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
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30
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Azim KF, Hasan M, Hossain MN, Somana SR, Hoque SF, Bappy MNI, Chowdhury AT, Lasker T. Immunoinformatics approaches for designing a novel multi epitope peptide vaccine against human norovirus (Norwalk virus). INFECTION GENETICS AND EVOLUTION 2019; 74:103936. [PMID: 31233780 DOI: 10.1016/j.meegid.2019.103936] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 06/18/2019] [Accepted: 06/20/2019] [Indexed: 12/19/2022]
Abstract
Norovirus is known as a major cause of several acute gastroenteritis (AGE) outbreaks each year. A study was conducted to develop a unique multi epitope subunit vaccine against human norovirus by adopting reverse vaccinology approach. The entire viral proteome of Norwalk virus was retrieved and allowed for further in silico study to predict highly antigenic epitopes through antigenicity, transmembrane topology screening, allergenicity assessment, toxicity analysis, population coverage analysis and molecular docking approach. Capsid protein VP1 and protein VP2 were identified as most antigenic viral proteins which generated a plethora of antigenic epitopes. Physicochemical properties and secondary structure of the designed vaccine were assessed to ensure its thermostability, hydrophilicity, theoretical PI and structural behavior. Molecular docking analysis of the refined vaccine with different MHCs and human immune TLR8 receptor demonstrated higher binding interaction as well. Complexed structure of the modeled vaccine and TLR8 showed minimal deformability at molecular level. The designed construct was reverse transcribed and adapted for E. coli strain K12 prior to insertion within pET28a(+) vector for its heterologous cloning and expression, and sequence of vaccine constructs showed no similarity with human proteins. However, the study could initiate in vitro and in vivo studies regarding effective vaccine development against human norovirus.
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Affiliation(s)
- Kazi Faizul Azim
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet 3100, Bangladesh; Department of Microbial Biotechnology, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Mahmudul Hasan
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet 3100, Bangladesh; Department of Pharmaceuticals and Industrial Biotechnology, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Md Nazmul Hossain
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet 3100, Bangladesh; Department of Microbial Biotechnology, Sylhet Agricultural University, Sylhet 3100, Bangladesh.
| | - Saneya Risa Somana
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Syeda Farjana Hoque
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Md Nazmul Islam Bappy
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Anjum Taiebah Chowdhury
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Tahera Lasker
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet 3100, Bangladesh
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31
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Hasan M, Azim KF, Begum A, Khan NA, Shammi TS, Imran AS, Chowdhury IM, Urme SRA. Vaccinomics strategy for developing a unique multi-epitope monovalent vaccine against Marburg marburgvirus. INFECTION GENETICS AND EVOLUTION 2019; 70:140-157. [DOI: 10.1016/j.meegid.2019.03.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 02/09/2019] [Accepted: 03/04/2019] [Indexed: 12/23/2022]
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32
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Chen Y, Wang G, Cai H, Sun Y, Ouyang L, Liu B. Deciphering the Rules of in Silico Autophagy Methods for Expediting Medicinal Research. J Med Chem 2019; 62:6831-6842. [PMID: 30888814 DOI: 10.1021/acs.jmedchem.8b01673] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Autophagy is a highly evolutionarily conserved cellular catabolic process responsible for degradation of damaged organelles and long-lived proteins. It is not surprising that scientific interest in the connection of autophagy and diseases has been growing. Over the past 2 decades, many new experimental approaches have been emerging in the field of targeting autophagy for medicinal research. Interestingly, in addition to experimental methods, a number of databases, Web servers, mathematics models, omics approaches, and systems biology network approaches related to autophagy have become available online, which may be collectively considered to be "in silico autophagy methods" for expediting current medicinal research. Thus, we have summarized a series of relevant in silico autophagy approaches for promoting the most appropriate usage of these resources for potential therapeutic purposes.
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Affiliation(s)
- Yi Chen
- State Key Laboratory of Biotherapy and Cancer Center and Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu 610041 , China
| | - Guan Wang
- State Key Laboratory of Biotherapy and Cancer Center and Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu 610041 , China
| | - Haoyang Cai
- Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences , Sichuan University , Chengdu 610064 , China
| | - Yang Sun
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Biotechnology and Pharmaceutical Sciences, School of Life Sciences , Nanjing University , Nanjing 210023 , China
| | - Liang Ouyang
- State Key Laboratory of Biotherapy and Cancer Center and Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu 610041 , China
| | - Bo Liu
- State Key Laboratory of Biotherapy and Cancer Center and Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu 610041 , China
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33
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Nuta GC, Gilad Y, Gershoni M, Sznajderman A, Schlesinger T, Bialik S, Eisenstein M, Pietrokovski S, Kimchi A. A cancer associated somatic mutation in LC3B attenuates its binding to E1-like ATG7 protein and subsequent lipidation. Autophagy 2019; 15:438-452. [PMID: 30238850 PMCID: PMC6351123 DOI: 10.1080/15548627.2018.1525476] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 08/30/2018] [Accepted: 09/14/2018] [Indexed: 02/01/2023] Open
Abstract
Macroautophagy/autophagy is a conserved catabolic process that maintains cellular homeostasis under basal growth and stress conditions. In cancer, autophagy can either prevent or promote tumor growth, at early or advanced stages, respectively. We screened public databases to identify autophagy-related somatic mutations in cancer, using a computational approach to identify cancer mutational target sites, employing exact statistics. The top significant hit was a missense mutation (Y113C) in the MAP1LC3B/LC3B (microtubule associated protein 1 light chain 3 beta) protein, which occurred at a significant frequency in cancer, and was detected in early stages in primary tumors of patients with known tumor lineage. The mutation reduced the formation of GFP-LC3B puncta and attenuated LC3B lipidation during Torin1-induced autophagy. Its effect on the direct physical interaction of LC3B with each of the 4 proteins that control its maturation or lipidation was tested by applying a protein-fragment complementation assay and co-immunoprecipitation experiments. Interactions with ATG4A and ATG4B proteases were reduced, yet without perturbing the cleavage of mutant LC3B. Most importantly, the mutation significantly reduced the interaction with the E1-like enzyme ATG7, but not the direct interaction with the E2-like enzyme ATG3, suggesting a selective perturbation in the binding of LC3B to some of its partner proteins. Structure analysis and molecular dynamics simulations of LC3B protein and its mutant suggest that the mutation changes the conformation of a loop that has several contact sites with ATG4B and the ATG7 homodimer. We suggest that this loss-of-function mutation, which attenuates autophagy, may promote early stages of cancer development.
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Affiliation(s)
- Gal Chaim Nuta
- Departments of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Yuval Gilad
- Departments of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Moran Gershoni
- Departments of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Arielle Sznajderman
- Departments of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Tomer Schlesinger
- Departments of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Shani Bialik
- Departments of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Miriam Eisenstein
- Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Shmuel Pietrokovski
- Departments of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Adi Kimchi
- Departments of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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34
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Hasan M, Ghosh PP, Azim KF, Mukta S, Abir RA, Nahar J, Hasan Khan MM. Reverse vaccinology approach to design a novel multi-epitope subunit vaccine against avian influenza A (H7N9) virus. Microb Pathog 2019; 130:19-37. [PMID: 30822457 DOI: 10.1016/j.micpath.2019.02.023] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 02/20/2019] [Accepted: 02/21/2019] [Indexed: 12/18/2022]
Abstract
H7N9, a novel strain of avian origin influenza was the first recorded incidence where a human was transited by a N9 type influenza virus. Effective vaccination against influenza A (H7N9) is a major concern, since it has emerged as a life threatening viral pathogen. Here, an in silico reverse vaccinology strategy was adopted to design a unique chimeric subunit vaccine against avian influenza A (H7N9). Induction of humoral and cell-mediated immunity is the prime concerned characteristics for a peptide vaccine candidate, hence both T cell and B cell immunity of viral proteins were screened. Antigenicity testing, transmembrane topology screening, allergenicity and toxicity assessment, population coverage analysis and molecular docking approach were adopted to generate the most antigenic epitopes of avian influenza A (H7N9) proteome. Further, a novel subunit vaccine was designed by the combination of highly immunogenic epitopes along with suitable adjuvant and linkers. Physicochemical properties and secondary structure of the designed vaccine were assessed to ensure its thermostability, h ydrophilicity, theoretical PI and structural behavior. Homology modeling, refinement and validation of the designed vaccine allowed to construct a three dimensional structure of the predicted vaccine, further employed to molecular docking analysis with different MHC molecules and human immune TLR8 receptor present on lymphocyte cells. Moreover, disulfide engineering was employed to lessen the high mobility region of the designed vaccine in order to extend its stability. Furthermore, we investigated the molecular dynamic simulation of the modeled subunit vaccine and TLR8 complexed molecule to strengthen our prediction. Finally, the suggested vaccine was reverse transcribed and adapted for E. coli strain K12 prior to insertion within pET28a(+) vector for checking translational potency and microbial expression.
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Affiliation(s)
- Mahmudul Hasan
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh; Department of Pharmaceuticals and Industrial Biotechnology, Sylhet Agricultural University, Sylhet, 3100, Bangladesh.
| | - Progga Paromita Ghosh
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | - Kazi Faizul Azim
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | - Shamsunnahar Mukta
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh; Department of Plant and Environmental Biotechnology, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | - Ruhshan Ahmed Abir
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Jannatun Nahar
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Mohammad Mehedi Hasan Khan
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh; Department of Biochemistry and Chemistry, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
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35
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Zhu M, Song X, Chen P, Wang W, Wang B. dbHDPLS: A database of human disease-related protein-ligand structures. Comput Biol Chem 2019; 78:353-358. [PMID: 30665056 DOI: 10.1016/j.compbiolchem.2018.12.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 12/11/2018] [Accepted: 12/30/2018] [Indexed: 12/31/2022]
Abstract
Protein-ligand complexes perform specific functions, most of which are related to human diseases. The database, called as human disease-related protein-ligand structures (dbHDPLS), collected 8833 structures which were extracted from protein data bank (PDB) and other related databases. The database is annotated with comprehensive information involving ligands and drugs, related human diseases and protein-ligand interaction information, with the information of protein structures. The database may be a reliable resource for structure-based drug target discoveries and druggability predictions of protein-ligand binding sites, drug-disease relationships based on protein-ligand complex structures. It can be publicly accessed at the website: http://DeepLearner.ahu.edu.cn/web/dbDPLS/.
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Affiliation(s)
- Muchun Zhu
- Institutes of Physical Science and Information Technology, Anhui University, 230601 Hefei, Anhui, China
| | - Xiaoping Song
- Institutes of Physical Science and Information Technology, Anhui University, 230601 Hefei, Anhui, China
| | - Peng Chen
- School of Electrical and Information Engineering, Anhui University of Technology, 243032 Ma'anshan, Anhui, China; Institutes of Physical Science and Information Technology, Anhui University, 230601 Hefei, Anhui, China.
| | - Wenyan Wang
- School of Electrical and Information Engineering, Anhui University of Technology, 243032 Ma'anshan, Anhui, China
| | - Bing Wang
- School of Electrical and Information Engineering, Anhui University of Technology, 243032 Ma'anshan, Anhui, China.
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Saini S, Jyoti-Thakur C, Kumar V, Suhag A, Jakhar N. In silico mutational analysis and identification of stability centers in human interleukin-4. MOLECULAR BIOLOGY RESEARCH COMMUNICATIONS 2018; 7:67-76. [PMID: 30046620 PMCID: PMC6054777 DOI: 10.22099/mbrc.2018.28855.1310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Interleukin-4 (IL-4) is a multifunctional cytokine that plays a critical role in apoptosis, differentiation and proliferation. The intensity of IL4 response depends upon binding to its receptor, IL-4R. The therapeutic efficiency of interleukins can be increased by generating structural mutants having greater stability. In the present work, attempts were made to increase the stability of human IL-4 using in-silico site directed mutagenesis. Different orthologous sequences of IL4 from Pan troglodytes, Aotusnigriceps, Macacamulatta, Papiohamadryas, Chlorocebusaethiops, Vicugnapacos, Susscrofa and Homo sapiens were aligned using Clustal Omega that revealed the conserved and non-conserved positions. For each non-conserved position, possible favorable and stabilizing mutations were found using CUPSAT with predicted ΔΔG (kcal/mol). The one with highest ΔΔG (kcal/mol) among all possible mutations, for each non-conserved position was selected and introduced manually in human IL-4 sequence resulting in multiple mutants of IL-4. Mutant proteins were modeled using structure of IL4 (PDB ID: 2B8U) as a template by SWISS MODEL. The mutants A49L and Q106T were identified to have stability centre using SCide. Molecular dynamics and docking analysis also confirmed the mutants stability and binding respectively. Mutants A49L and Q106T had -7.580079 kcal/mol and -39.418124 kcal/mol respectively lesser energy value than the wild type IL4. The result suggested that, the stability of human IL-4 has been increased by mutation.
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Affiliation(s)
- Sandeep Saini
- Department of Bioinformatics, G.G.D.S.D. College, Chandigarh, India
| | | | - Varinder Kumar
- Department of Bioinformatics, G.G.D.S.D. College, Chandigarh, India
| | - Akshay Suhag
- Department of Bioinformatics, G.G.D.S.D. College, Chandigarh, India
| | - Niharika Jakhar
- Department of Bioinformatics, G.G.D.S.D. College, Chandigarh, India
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Pires ADO, Queiroz GDA, de Jesus Silva M, da Silva RR, da Silva HBF, Carneiro NVQ, Fonseca HF, de Santana MBR, Nascimento RS, Alcântara-Neves NM, Costa GNDO, Costa RDS, Barreto ML, Figueiredo CA. Polymorphisms in the DAD1 and OXA1L genes are associated with asthma and atopy in a South American population. Mol Immunol 2018; 101:294-302. [PMID: 30032071 DOI: 10.1016/j.molimm.2018.07.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 04/03/2018] [Accepted: 07/07/2018] [Indexed: 12/13/2022]
Abstract
Atopic asthma, which is characterized by the chronic inflammation and morbidity of airways, is a disease of great complexity, and multiple genetic and environmental factors are involved in its etiology. In the first genome-wide association study (GWAS) conducted in Brazil for asthma, a positive association was found between atopic asthma and a variant (rs1999071), which is located between the DAD1 and OXA1L genes, although neither gene has previously been reported to be associated with asthma or allergies. The DAD1 gene is involved in the regulation of programmed cell death, and OXA1L is involved in biogenesis and mitochondrial oxidative phosphorylation. This study aimed to evaluate how polymorphisms in DAD1 and OXA1L are associated with asthma and markers of atopy in individuals from the Salvador cohort of the SCAALA (Social Change Asthma and Allergy in Latin America) program. The DNA of 1220 individuals was genotyped using the Illumina 2.5 Human Omni Bead chip. Logistic regression analyses were performed with PLINK 1.9 software to verify the association between DAD1 and OXA1L polymorphisms and asthma and atopic markers, adjusted for sex, age, helminth infections and ancestry markers, using an additive model. The DAD1 and OXA1L genes were associated with some of the evaluated phenotypes, such as asthma, skin prick test (SPT), specific IgE for aeroallergens, and Th1/Th2-type cytokine production. Using qPCR, as well as in silico gene expression analysis, we have demonstrated that some of the polymorphisms in both genes are able to affect their respective gene expression levels. In addition, DAD1 was over-expressed in asthmatic patients when compared with controls. Thus, our findings demonstrate that variants in both the DAD1 and OXA1L genes may affect atopy and asthma in a Latin American population with a high prevalence of asthma.
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Affiliation(s)
- Anaque de Oliveira Pires
- Laboratory of Immunopharmacology and Molecular Biology, Federal University of Bahia, Salvador, Brazil
| | - Gerson de Almeida Queiroz
- Laboratory of Immunopharmacology and Molecular Biology, Federal University of Bahia, Salvador, Brazil
| | - Milca de Jesus Silva
- Laboratory of Immunopharmacology and Molecular Biology, Federal University of Bahia, Salvador, Brazil
| | - Raimon Rios da Silva
- Laboratory of Immunopharmacology and Molecular Biology, Federal University of Bahia, Salvador, Brazil
| | | | | | - Héllen Freitas Fonseca
- Laboratory of Immunopharmacology and Molecular Biology, Federal University of Bahia, Salvador, Brazil
| | | | - Regina Santos Nascimento
- Laboratory of Immunopharmacology and Molecular Biology, Federal University of Bahia, Salvador, Brazil
| | | | | | - Ryan Dos Santos Costa
- Laboratory of Immunopharmacology and Molecular Biology, Federal University of Bahia, Salvador, Brazil
| | - Maurício L Barreto
- Gonçalo Moniz Research Center, Oswaldo Cruz Foundation, Salvador, Brazil
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Lee MR, Yoo WG, Kim YJ, Chung EJ, Cho SH, Ju JW. Venom allergen-like protein 28 in Clonorchis sinensis: four epitopes on its surface and the potential role of Cys124 for its conformational stability. Parasitol Res 2018; 117:2521-2530. [PMID: 29876859 DOI: 10.1007/s00436-018-5941-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 05/23/2018] [Indexed: 11/26/2022]
Abstract
Venom allergen-like (VAL) proteins are important to host-parasite interactions. We previously demonstrated that a Clonorchis sinensis VAL (CsVAL) protein-derived synthetic peptide suppresses allergic and inflammatory responses. However, little is known regarding the physicochemical and antigenic properties of CsVAL proteins. Here, we identified a novel 194 amino acid VAL protein, named C. sinensis VAL 28 (CsVAL28), and characterized its functional motifs and structural details as a new member of the CAP superfamily. Unlike members of the Schistosoma mansoni VAL (SmVAL) family, CsVAL28 has a single CAP1 motif and six highly conserved disulfide bond-forming cysteines. Tertiary models of wild-type CsVAL28 and mutants were built using SmVAL4 as template via homology modeling. Normal mode analysis predicted that disulfide bond breaking by mutation of cysteine 124 to serine would greatly affect protein mobility. Four major immunoreactive linear epitopes were identified in the surface-exposed region or its vicinity via epitope mapping, using sera from clonorchiasis patients and healthy controls. Our findings provide in-depth knowledge on the structure-function properties of VAL proteins and may help determine highly antigenic regions for developing new diagnostic approaches.
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Affiliation(s)
- Myoung-Ro Lee
- Division of Vectors and Parasitic Diseases, Center for Laboratory control of Infectious Diseases, Korea Centers for Disease Control and Prevention, Chungbuk, 28159, Republic of Korea
| | - Won Gi Yoo
- Division of Vectors and Parasitic Diseases, Center for Laboratory control of Infectious Diseases, Korea Centers for Disease Control and Prevention, Chungbuk, 28159, Republic of Korea
- Department of Medical Environmental Biology, Chung-Ang University College of Medicine, Seoul, 06974, Republic of Korea
| | - Yu Jung Kim
- Division of Vectors and Parasitic Diseases, Center for Laboratory control of Infectious Diseases, Korea Centers for Disease Control and Prevention, Chungbuk, 28159, Republic of Korea
| | - Eun Ju Chung
- Division of Vectors and Parasitic Diseases, Center for Laboratory control of Infectious Diseases, Korea Centers for Disease Control and Prevention, Chungbuk, 28159, Republic of Korea
| | - Shin-Hyeong Cho
- Division of Vectors and Parasitic Diseases, Center for Laboratory control of Infectious Diseases, Korea Centers for Disease Control and Prevention, Chungbuk, 28159, Republic of Korea
| | - Jung-Won Ju
- Division of Vectors and Parasitic Diseases, Center for Laboratory control of Infectious Diseases, Korea Centers for Disease Control and Prevention, Chungbuk, 28159, Republic of Korea.
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