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  1. Article ; Online: In silico design of an epitope-based vaccine against choline binding protein A of Streptococcus pneumoniae

    Meherunnesa Munia / Shafi Mahmud / Mohammed Mohasin / K.M. Kaderi Kibria

    Informatics in Medicine Unlocked, Vol 23, Iss , Pp 100546- (2021)

    2021  

    Abstract: Streptococcus pneumoniae (Pneumococcus) accounts for a major global health burden that causes bacterial pneumonia, sepsis, otitis media, and meningitis. It is responsible for great morbidity and mortality globally. Available pneumonia vaccines are either ...

    Abstract Streptococcus pneumoniae (Pneumococcus) accounts for a major global health burden that causes bacterial pneumonia, sepsis, otitis media, and meningitis. It is responsible for great morbidity and mortality globally. Available pneumonia vaccines are either carbohydrate-based vaccines or not protective against specific serotypes. Besides, antibiotic resistance to pneumococci justifies further attention to explore new vaccine candidates. The invariant peptide-based vaccines are not only immunogenic for all age groups but also protective against all serotypes of pneumococci. Initially, we searched for potential vaccine candidates of pneumococcus through literature mining. We found Choline binding protein A (CbpA) as a potential immunogenic extracellular protein. Next we applied the immunoinformatic approach to design a multi-epitope based vaccine (MEV) candidate of CbpA against pneumococcus. Furthermore, the protein sequence revealed the immunogenic T-cell epitopes of CbpA. The affinity between the T-cell epitope and MHC molecule was evaluated by Molecular docking (MD) analyses. We found a single 15-mer T-cell epitope (AMATGWLQYNGSWYY), which has not only affinity for both MHC class I and class II but also has the highest population coverage. Besides, the B-cell and IFNγ-inducing epitopes were also selected. All the peptides were assessed for conservancy, allergenicity, immunogenicity, and hydrophobicity. Finally, we assembled the best T-cell, B-cell, and IFNγ-inducing epitopes to make an MEV. The docking and MD simulation study revealed a strong affinity between the MEV and Toll-like receptors. Therefore, we propose that MEV of CbpA could be a novel vaccine candidate, which may induce both humoral and cellular immune responses to non-serotype-specific pneumococcus.
    Keywords Streptococcus pneumoniae ; MHC ; Choline binding protein A (CbpA) ; Epitope based vaccine ; Computer applications to medicine. Medical informatics ; R858-859.7
    Subject code 570
    Language English
    Publishing date 2021-01-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Identification and in silico molecular modelling study of newly isolated Bacillus subtilis SI-18 strain against S9 protein of Rhizoctonia solani

    Md. Samiul Islam / Shafi Mahmud / Razia Sultana / Wubei Dong

    Arabian Journal of Chemistry, Vol 13, Iss 12, Pp 8600-

    2020  Volume 8612

    Abstract: The numerous bioactive components from Bacillus subtilis are commonly used as antimicrobial agents for reducing plant diseases caused by fungal pathovars. In this study, we isolated and identified B. subtilis SI-18 strain from twenty isolates of ... ...

    Abstract The numerous bioactive components from Bacillus subtilis are commonly used as antimicrobial agents for reducing plant diseases caused by fungal pathovars. In this study, we isolated and identified B. subtilis SI-18 strain from twenty isolates of rhizosphere soil through morphological and molecular approaches, and explored its inhibitory activities against Rhizoctonia solani. According to morphological features and 16S rRNA and gyrB gene sequence analysis, B. subtilis SI-18 strain was identified. Additionally, the culture filtrate of B. subtilis SI-18 resulted in the suppression of R. solani mycelium growth and material leakage from the cells. Then, we have performed homology modelling and molecular docking study of S9 protein from R. solani where three potential compounds (D1, D2, and D3) were identified among 134 antimicrobial compounds derived from B. subtilis group based on higher binding energy and interaction at the active grove of the target protein. The D1 compound creates alkyl bond at Val48 whereas D2 also binds with Val48 by creating hydrogen bond. On the other hand, two hydrogen bonds were observed at Val48 and Ile52 by D3, which might be responsible for possible blocking of the target S9 protein of R. solani. To validate the docking study and understand the change in drug-ligand conformation, molecular dynamics simulation was assessed where rigid conformation was found for D1, D2 and D3 complexes. Moreover, ADMET study confirms that no toxicity and carcinogenicity were found for screened compounds. Based on our studies, we demonstrated that compounds D1, D2, and D3 derived from B. subtilis can be a potential inhibitor of S9 protein of R. solani that might be a possible strategy for fungal disease prevention.
    Keywords Bacillus subtilis ; Antimicrobial potential ; Rhizoctonia solani ; S9 protein ; Molecular docking ; Chemistry ; QD1-999
    Subject code 500
    Language English
    Publishing date 2020-12-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: In silico prediction of a highly immunogenic and conserved epitope against Zika Virus

    Debasish Paul / Imdadul Haque Sharif / Abu Sayem / Hossain Ahmed / Md. Abu Saleh / Shafi Mahmud

    Informatics in Medicine Unlocked, Vol 24, Iss , Pp 100613- (2021)

    2021  

    Abstract: Zika virus (ZIKV) is an arboviral pathogen that belongs to the Flaviviridae subgroup and is a contemporary global concern. Recent epidemic outbreaks in Brazil have indicated that ZIKV could be responsible for post-infection neurological disorders in ... ...

    Abstract Zika virus (ZIKV) is an arboviral pathogen that belongs to the Flaviviridae subgroup and is a contemporary global concern. Recent epidemic outbreaks in Brazil have indicated that ZIKV could be responsible for post-infection neurological disorders in infants, resulting in ZIKV being considered a major threat to global health. Unfortunately, no vaccine is yet available to prevent the spread of this virus. In this study, we have applied an in silico approach to the identification of B-cell epitopes in the ZIKV genome. By utilizing currently available genomic data and applying multiple sequence alignments and the Immune Epitope Database (IDEB) tools, a LEFYSYKKSG epitope was identified in a highly conserved peptide region of the ZIKV polyprotein. The antigenicity, allergenicity, and affinity of the B-cell epitope were evaluated, and significant B-cell affinity against ZIKV was identified. This highly conserved epitope can be used to develop a peptide-based vaccine and can also be applied toward the development of a monoclonal antibody (mAb) for therapeutic or diagnostic purposes against ZIKV.
    Keywords Zika virus ; B-Cell epitope ; Antigenicity ; Allergenicity affinity ; Vaccine ; Global solution ; Computer applications to medicine. Medical informatics ; R858-859.7
    Subject code 570
    Language English
    Publishing date 2021-01-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Structure-based design of new diclofenac

    Monir Uzzaman / Md. Kamrul Hasan / Shafi Mahmud / Kaniz Fatema / Mohammed Mahbubul Matin

    Informatics in Medicine Unlocked, Vol 25, Iss , Pp 100677- (2021)

    Physicochemical, spectral, molecular docking, dynamics simulation and ADMET studies

    2021  

    Abstract: Diclofenac, a nonsteroidal anti-inflammatory drug, is commonly prescribed for the analgesic, antipyretic and anti-inflammation treatment. It is effectively used in acute and chronic pain. It inhibits the prostaglandin synthesis by blocking cyclooxygenase ...

    Abstract Diclofenac, a nonsteroidal anti-inflammatory drug, is commonly prescribed for the analgesic, antipyretic and anti-inflammation treatment. It is effectively used in acute and chronic pain. It inhibits the prostaglandin synthesis by blocking cyclooxygenase (COX). However, it shows some crucial side effects like renal, gastrointestinal and cardiovascular injury to the human and other living things. It also causes gastrointestinal side effects like bleeding and perforation if taken at higher dose for a long period of time. Liver toxicity is also another issue related to oral diclofenac. To improve its safety profile, an attempt has been taken to design some new potential drug to reduce the side effects with better medicinal action. The insertion of new functional groups such as CH3, OCH3, F, CF3, OCF3, Cl, OH, COOH, NH2, CH2NH2, CONH2, NHCOCH3 at the different positions of its core structure significantly enhance the chemical and biological performance. Chemical, physical and spectral calculation has been performed by geometry optimization to characterize the newly designed structures. Molecular docking and dynamics simulation have been performed against human prostaglandin synthase protein (PDB ID: 5F19) to predict binding affinity, bonding interaction and stability of protein-drug complex. ADMET predictions have been studied to search for their pharmacokinetic properties like absorption, metabolism and toxicity. Physicochemical and spectral data support the new structural conformation. Molecular docking and dynamics studies disclose improved medicinal effect and pharmacokinetic prediction suggest their reduced side effects and non-carcinogenic properties than the parent drug which lead to develop the novel drug with improved clinical safety.
    Keywords Diclofenac ; Computer-aided drug design ; Molecular docking ; Dynamics simulation ; Biological and drug likeness evaluation ; ADMET ; Computer applications to medicine. Medical informatics ; R858-859.7
    Subject code 006 ; 540
    Language English
    Publishing date 2021-01-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Identification of Zinc-Binding Inhibitors of Matrix Metalloproteinase-9 to Prevent Cancer Through Deep Learning and Molecular Dynamics Simulation Approach

    Shalini Mathpal / Priyanka Sharma / Tushar Joshi / Veena Pande / Shafi Mahmud / Mi-Kyung Jeong / Ahmad J. Obaidullah / Subhash Chandra / Bonglee Kim

    Frontiers in Molecular Biosciences, Vol

    2022  Volume 9

    Abstract: The overexpression of matrix metalloproteinase-9 (MMP-9) is associated with tumor development and angiogenesis, and hence, it has been considered an attractive drug target for anticancer therapy. To assist in drug design endeavors for MMP-9 targets, an ... ...

    Abstract The overexpression of matrix metalloproteinase-9 (MMP-9) is associated with tumor development and angiogenesis, and hence, it has been considered an attractive drug target for anticancer therapy. To assist in drug design endeavors for MMP-9 targets, an in silico study was presented to investigate whether our compounds inhibit MMP-9 by binding to the catalytic domain, similar to their inhibitor or not. For that, in the initial stage, a deep-learning algorithm was used for the predictive modeling of the CHEMBL321 dataset of MMP-9 inhibitors. Several regression models were built and evaluated based on R2, MAE MSE, RMSE, and Loss. The best model was utilized to screen the drug bank database containing 9,102 compounds to seek novel compounds as MMP-9 inhibitors. Then top high score compounds were selected for molecular docking based on the comparison between the score of the reference molecule. Furthermore, molecules having the highest docking scores were selected, and interaction mechanisms with respect to S1 pocket and catalytic zinc ion of these compounds were also discussed. Those compounds, involving binding to the catalytic zinc ion and the S1 pocket of MMP-9, were considered preferentially for molecular dynamics studies (100 ns) and an MM-PBSA (last 30 ns) analysis. Based on the results, we proposed several novel compounds as potential candidates for MMP-9 inhibition and investigated their binding properties with MMP-9. The findings suggested that these compounds may be useful in the design and development of MMP-9 inhibitors in the future.
    Keywords cancer ; MMP-9 ; deep learning ; drug bank compounds ; MD simulation ; Biology (General) ; QH301-705.5
    Subject code 540
    Language English
    Publishing date 2022-03-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: In vitro antioxidant and cytotoxicity activities and in silico anticancer property of methanolic leaf extract of Leucas indica

    Tasmina Ferdous Susmi / Md Moshiur Rahman Khan / Atikur Rahman / Shafi Mahmud / Md Abu Saleh / Md Abu Reza / Md Sifat Rahi

    Informatics in Medicine Unlocked, Vol 31, Iss , Pp 100963- (2022)

    2022  

    Abstract: The investigation of traditional medicinal plants is gaining prime importance day by day due to having a wide range of bioactive phytochemicals. The presence of diverse bioactive compounds makes medicinal plants more demandable for curing several ... ...

    Abstract The investigation of traditional medicinal plants is gaining prime importance day by day due to having a wide range of bioactive phytochemicals. The presence of diverse bioactive compounds makes medicinal plants more demandable for curing several diseases, such as inflammatory diseases, diabetes, and cancer. Leucas indica is commonly found throughout Bangladesh and traditionally used for medical purposes because of its great medicinal value to the folks. The present study addresses the evaluation of in vitro qualitative phytochemical, antioxidant, and cytotoxicity activities as well as in silico anticancer activity of methanolic leaf extract. Several standard methods were used for phytochemical analysis, which showed the presence of different phytochemicals. The plant exhibited adequate antioxidant activities through DPPH and H2O2 free radical scavenging assays. Moreover, promising cytotoxicity activity was estimated through a brine shrimp lethality assay. In addition, the present work emphasizes the in silico analysis, which finds the anticancer activity of the experimental plant based on pharmacokinetic analysis, molecular docking, and MD simulation. Four phytochemicals of the plant were selected from the literature and docked against two important protein kinases (AMPK and CDK6) that have a role in cancer progression. The docking revealed an encouraging binding score with a maximum score of 9.2 kCal/mol, where all the ligand-protein complexes showed stable conditions during simulation. According to this analysis, it can be believed that the selected ligands indicate promising anticancer activity. Moreover, the comprehensive analysis of both in vitro and in silico data shows that the leaf could be a potent source of drug and could serve as an effective therapeutic in the future.
    Keywords Leucas indica ; Antioxidant ; Cytotoxicity ; ADMET ; Molecular docking ; MD Simulation ; Computer applications to medicine. Medical informatics ; R858-859.7
    Subject code 580
    Language English
    Publishing date 2022-01-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: In search of novel inhibitors of anti-cancer drug target fibroblast growth factor receptors

    A M U B Mahfuz / Md. Arif Khan / Suvro Biswas / Shamima Afrose / Shafi Mahmud / Newaz Mohammed Bahadur / Firoz Ahmed

    Arabian Journal of Chemistry, Vol 15, Iss 7, Pp 103882- (2022)

    Insights from virtual screening, molecular docking, and molecular dynamics

    2022  

    Abstract: Fibroblast growth factor receptors (FGFR) are an essential player in oncogenesis and tumor progression. LY2874455 was identified as a pan-FGFR inhibitor and has gone through phase I clinical trial. In the current study, virtual screening was conducted ... ...

    Abstract Fibroblast growth factor receptors (FGFR) are an essential player in oncogenesis and tumor progression. LY2874455 was identified as a pan-FGFR inhibitor and has gone through phase I clinical trial. In the current study, virtual screening was conducted against the PubChem database using a pharmacophore model generated from the crystal structure of FGFR4 inhibited by LY2874455. PubChem 137300327 was identified as the most suitable compound from this screening. Later, molecular docking and molecular dynamics studies conducted with FGFRs corroborated the initial finding. Analysis of ADMET properties disclosed that LY2874455 and PubChem 137300327 share alike properties. Our study suggests that PubChem 137300327 is a potential pan-FGFR inhibitor and can be exploited to treat different cancers following validation in proper wet-lab experiments and study in animal cancer models. This compound also follows Lipinski’s rules and can be used as a lead compound to synthesize more effective anticancer compounds.
    Keywords Fibroblast growth factor receptor ; FGFR ; Anti-cancer drug ; Chemotherapy ; Chemistry ; QD1-999
    Subject code 540
    Language English
    Publishing date 2022-07-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Biochemical and in silico study of leaf and bark extracts from Aphanamixis polystachya against common pathogenic bacteria

    Gobindo Kumar Paul / Shafi Mahmud / Md. Mehedi Hasan / Shahriar Zaman / Md. Salah Uddin / Md. Abu Saleh

    Saudi Journal of Biological Sciences, Vol 28, Iss 11, Pp 6592-

    2021  Volume 6605

    Abstract: Aphanamixis polystachya may be a natural, renewable resource against antibiotic-resistant bacterial infections. The antibacterial activity of A. polystachya leaf and bark extracts was investigated against three antibiotic-resistant bacterial species and ... ...

    Abstract Aphanamixis polystachya may be a natural, renewable resource against antibiotic-resistant bacterial infections. The antibacterial activity of A. polystachya leaf and bark extracts was investigated against three antibiotic-resistant bacterial species and one fungus. Methanolic leaf extract showed only limited antibacterial activity but both methanolic and aqueous bark extract showed high antimicrobial activity. In an antioxidant activity test, leaf and bark extracts exhibited 50% free radical scavenging at a concentration of 107.14 ± 3.14 μg/mL and 97.13 ± 3.05 μg/mL, respectively, indicating that bark extracts offer more antioxidative activity than leaf extracts. Bark extracts also showed lower toxicity than leaf extracts. This suggests that bark extracts may offer greater development potential than leaf extracts. The molecular dynamics were also investigated through the simulated exploration of multiple potential interactions to understand the interaction dynamics (root-mean-square deviation, solvent-accessible surface area, radius of gyration, and the hydrogen bonding of chosen compounds to protein targets) and possible mechanisms of inhibition. This molecular modeling of compounds derived from A. polystachya revealed that inhibition may occur by binding to the active sites of the target proteins of the tested bacterial strains. A. polystachya bark extract may be used as a natural source of drugs to control antibiotic-resistant bacteria.
    Keywords Aphanamixis polystachya extract ; Antibiotic resistance ; Antimicrobial activity ; Antioxidant activity ; Cytotoxicity ; Molecular docking ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2021-11-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: Physicochemical, spectral, molecular docking and ADMET studies of Bisphenol analogues; A computational approach

    Monir Uzzaman / Md. Kamrul Hasan / Shafi Mahmud / Abu Yousuf / Saidul Islam / Mohammad Nasir Uddin / Ayan Barua

    Informatics in Medicine Unlocked, Vol 25, Iss , Pp 100706- (2021)

    2021  

    Abstract: Bisphenols are widely used in polymer and packaging industries. But they are contaminating the environment and food chain by degradation, particularly affecting to the human endocrine system. Herein, we have investigated the physicochemical, spectral, ... ...

    Abstract Bisphenols are widely used in polymer and packaging industries. But they are contaminating the environment and food chain by degradation, particularly affecting to the human endocrine system. Herein, we have investigated the physicochemical, spectral, biological and pharmacokinetic properties of some selected bisphenol analogues utilizing computer-aided drug design methods. Geometry optimization has been performed by employing density functional theory with B3LYP/6-311g++ (d, p) basis set. Geometrical, thermodynamical, molecular orbital and electrostatic potential studies have been calculated to investigate their physical and chemical behavior. Meanwhile, FT-IR, Raman and UV-Vis's spectra have been measured and compared with the experimental values. Molecular docking and dynamics simulation studies have been performed against human estrogen-related receptor protein to investigate their binding affinity, mode and interactions with the receptor. ADMET prediction has been performed to compare their absorption, distribution, metabolism and toxicity. Among the studied analogues, Bis AF has the highest free energy and Bis E has highest binding affinity. Meanwhile, Bis S shows the highest dipole moment and the chemical reactivity. Most of them have inhibitory property to the CYP2C9 and Bis S shows the carcinogenic property. Based on the comparative physicochemical, spectral, biological and ADMET calculation, this study can be helpful to understand more deeply about their biochemical impact on the environment and human being.
    Keywords Bisphenols ; Endocrine disrupt ; Molecular docking and dynamics simulation ; ADMET ; Computer applications to medicine. Medical informatics ; R858-859.7
    Language English
    Publishing date 2021-01-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: In vitro and in silico approach of fungal growth inhibition by Trichoderma asperellum HbGT6-07 derived volatile organic compounds

    Md. Kamaruzzaman / Md. Samiul Islam / Shafi Mahmud / Shakil Ahmed Polash / Razia Sultana / Md. Amit Hasan / Chao Wang / Chunhao Jiang

    Arabian Journal of Chemistry, Vol 14, Iss 9, Pp 103290- (2021)

    2021  

    Abstract: The species of Trichoderma are one of the most frequently used natural biocontrol agent. This study, we identified isolate HbGT6-07 of Trichoderma asperellum and evaluated the antimicrobial effects both in vitro and in silico approaches. Tested 10% ... ...

    Abstract The species of Trichoderma are one of the most frequently used natural biocontrol agent. This study, we identified isolate HbGT6-07 of Trichoderma asperellum and evaluated the antimicrobial effects both in vitro and in silico approaches. Tested 10% concentrated culture filtrate of HbGT6-07 inhibited 98% of colony radial growth in B. cinerea (B05.10) as well as 91% of S. sclerotiorum (A367). HbGT6-07 was detected to produce volatile organic compounds (VOCs) with antifungal activity. In in-vitro dish-within-dish method (DwD), The HbGT6-07 VOCs effectively reduced colonial diameter, growth rate and sclerotia production by two virulent fungal pathogens. Moreover, the hyphal fragments of HbGT6-07 demonstrated successful mycelia growth suppression (97%) against infection oilseed rape leaves by hyphae of the two virulent fungal pathogens through competition. The mixed culture assay, exhibited that the isolate T. asperellum HbGT6-07 was significantly reduced the production and weight of sclerotia. The GC-MS analysis identified 32 VOCs derived from HbGT6-07. In addition, VOCs derived from HbGT6-07 were assessed against targeted protein of three fungal species; Aspergillus oryzae, Saccharomyces cerevisiae, Candida albicans via molecular docking. Butylated hydroxytolune and Beta-Cedrene had energy (−5.3 and −5.7 Kcal/mol) for targeted protein of Aspergillus oryzae and (−6.8 and −8.0 Kcal/mol) for Saccharomyces cerevisiae, whereas alpha-bergamotene and Beta-Cedrene exihbit energy (−7.5 and −7.4 Kcal/mol), respectively. The molecular dynamics study confirms the structural stability and rigidity of the docked complex through multiple descriptors from simulation trajectories. The above findings indicated that HbGT6-07 could attain competitive progress via production of VOCs and comprehensive mycelial growth.
    Keywords Trichoderma asperellum ; Biological control ; VOCs ; Docking ; Molecular dynamics ; Chemistry ; QD1-999
    Subject code 571
    Language English
    Publishing date 2021-09-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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