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Zengin G, Cetiz MV, Abul N, Gulcin I, Caprioli G, Piatti D, Ricciutelli M, Koyuncu I, Yuksekdag O, Bahşi M, Güler O, Aumeeruddy MZ, Mahomoodally MF. Establishing a link between the chemical composition and biological activities of Gladiolus italicus Mill. from the Turkish flora utilizing in vitro, in silico and network pharmacological methodologies. Toxicol Mech Methods 2024:1-21. [PMID: 39246014 DOI: 10.1080/15376516.2024.2397387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 08/14/2024] [Accepted: 08/18/2024] [Indexed: 09/10/2024]
Abstract
OBJECTIVES Five solvent extracts (n-hexane, ethyl acetate, ethanol, ethanol/water (70%), and water) of Gladiolus italicus Mill. from Turkey were evaluated for chemical and biological properties. METHODS Antioxidant activities, inhibitory properties against key enzymes involved in the etiology of chronic diseases were tested, as well as cytotoxic effects on different cell lines. Chemical characterization was also carried out to determine the most abundant compounds of each extract. RESULTS The highest total phenolic content (TPC) was observed in the water extract while highest TFC in ethanol/water extract. The most abundant compounds in the extracts were hyperoside (69041.06 mg kg-1), isoquercitrin (46239.49 mg kg-1), delphindin-3,5-diglucoside (42043.81 mg kg-1), myricetin (21486.61 mg kg-1), and kaempferol-3-glucoside (21199.76 mg kg-1). Molecular dynamic (MD) simulations confirmed the structural stability and dynamic conformational integrity of these complexes over a period of 100 ns. In network pharmacology, A total of 657 unique target genes were screened: 52 associated with programmed cell death-1 (PD-1), 85 with vascular endothelial growth factor receptor-2 (VEGFR2), and 130 with fibroblast growth factor receptor-2 (FGFR2), identifying crucial gene interactions for these proteins. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were conducted, revealing significant interactions and pathways such as the advanced glycation end products (AGE) and their receptors (RAGE) signaling pathway in diabetic complications and T- helper 17 (Th17) cell differentiation, among others. This elucidation of complex networks involving key genes like AKT Serine/Threonine Kinase 1 (AKT1), MYC proto-oncogene (MYC), tumor protein 53 (TP53), Interleukin 6 (IL6), and tumor necrosis factor (TNF) provides a promising foundation for the development of targeted therapies in the treatment of non-communicable diseases. CONCLUSION These results show that G. italicus could be a natural source of potent antioxidants and enzyme inhibitors which need to be further explored for the development of biopharmaceuticals.
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Affiliation(s)
- Gokhan Zengin
- Department of Biology, Faculty of Science, Selcuk University, Konya, Turkey
| | - Mehmet Veysi Cetiz
- Department of Bioinformatics, Biozentrum der Universität Würzburg, Würzburg, Germany
| | - Nurgul Abul
- Department of Chemistry, Faculty of Sciences, Ataturk University, Erzurum
| | - Ilhami Gulcin
- Department of Chemistry, Faculty of Sciences, Ataturk University, Erzurum
| | - Giovanni Caprioli
- CHemistry Interdisciplinary Project (CHip), School of Pharmacy, University of Camerino, Camerino, Italy
| | - Diletta Piatti
- CHemistry Interdisciplinary Project (CHip), School of Pharmacy, University of Camerino, Camerino, Italy
| | - Massimo Ricciutelli
- CHemistry Interdisciplinary Project (CHip), School of Pharmacy, University of Camerino, Camerino, Italy
| | - Ismail Koyuncu
- Department of Medical Biochemistry, Faculty of Medicine, Harran University, Sanliurfa, Turkey
| | - Ozgur Yuksekdag
- Department of Medical Biochemistry, Faculty of Medicine, Harran University, Sanliurfa, Turkey
| | - Muammer Bahşi
- Faculty of Education, Department of Primary Education, Firat University, Elazig, Turkey
| | - Osman Güler
- Pertek Sakine Genç Vocational School, Munzur University, Pertek, Tunceli, Turkey
| | | | - Mohamad Fawzi Mahomoodally
- Institute of Research and Development, Duy Tan University, Da Nang, Vietnam
- School of Engineering & Technology, Duy Tan University, Da Nang, Vietnam
- Laboratory of Natural Products and Medicinal Chemistry (LNPMC), Center for Global Health Research, Saveetha Medical College and Hospital, Saveetha Institute of Medical and Technical Sciences (SIMATS), Thandalam, India
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Adeyemi OE, Jaryum KH, Johnson TO. Elucidation and active ingredient identification of aqueous extract of Ficus exasperata Vahl leaf against bisphenol A-induced toxicity through in vivo and in silico assessments. In Silico Pharmacol 2024; 12:73. [PMID: 39144917 PMCID: PMC11319549 DOI: 10.1007/s40203-024-00248-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Accepted: 07/30/2024] [Indexed: 08/16/2024] Open
Abstract
Bisphenol A (BPA), an endocrine-disrupting chemical, poses significant health problems due to its induction of oxidative stress, inflammation, etc. Whereas Ficus exasperata Vahl leaf (FEVL) was reported for its ethnopharmacological properties against several ailments owing to its antioxidant, anti-inflammatory properties, etc. Here, we aim to elucidate and identify the bioactive compounds of aqueous extract of FEVL (AEFEVL) against BPA-induced toxicity using in vivo and in silico assessments. To determine the BPA toxicity mechanism and safe doses of AEFEVL, graded doses of BPA (0-400 μM) and AEFEVL (0-2.0 mg/10 g diets) were separately fed to flies to evaluate survival rates and specific biochemical markers. The mitigating effect of AEFEVL (0.5 and 1.0 mg/10 g diet) against BPA (100 and 200 μM)-induced toxicity in the flies after 7-day exposure was also carried out. Additionally, molecular docking analysis of BPA and BPA-o-quinone (BPAQ) against selected antioxidant targets, and HPLC-MS-revealed AEFEVL compounds against Keap-1 and IKKβ targets, followed by ADMET analysis, was conducted. Emergence rate, climbing ability, acetylcholinesterase, monoamine oxidase-B, and glutathione-S-transferase activities, and levels of total thiols, non-protein thiols, nitric oxide, protein carbonyl, malondialdehyde, and cell viability were evaluated. BPA-induced altered biochemical and behavioral parameters were significantly mitigated by AEFEVL in the flies (p < 0.05). BPAQ followed by BPA exhibited higher inhibitory activity, and epigallocatechin (EGC) showed the highest inhibitory activity among the AEFEVL compounds with desirable ADMET properties. Conclusively, our findings revealed that EGC might be responsible for the mitigative effect displayed by AEFEVL in BPA-induced toxicity in D. melanogaster. Graphical abstract
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Affiliation(s)
- Olugbenga Eyitayo Adeyemi
- Department of Biochemistry, Faculty of Basic Medical Sciences, College of Health Sciences, University of Jos, Jos, Nigeria
- Department of Biochemistry, Federal College of Medical Laboratory Sciences (Technology), Jos, Nigeria
| | - Kiri Hashimu Jaryum
- Department of Biochemistry, Faculty of Basic Medical Sciences, College of Health Sciences, University of Jos, Jos, Nigeria
| | - Titilayo Omolara Johnson
- Department of Biochemistry, Faculty of Basic Medical Sciences, College of Health Sciences, University of Jos, Jos, Nigeria
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3
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Shuvo MN, Halder SK, Alam N, Himel MK, Shil A. Developing phytocompound-based new drugs against multi-drug-resistant Staphylococcus aureus. ROYAL SOCIETY OPEN SCIENCE 2024; 11:231475. [PMID: 39050719 PMCID: PMC11265916 DOI: 10.1098/rsos.231475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 05/28/2024] [Accepted: 06/13/2024] [Indexed: 07/27/2024]
Abstract
Staphylococcus aureus, a prevalent component of the human microbiota, is associated with skin infections to life-threatening diseases, presenting challenges in treatment options and necessitating the development of effective treatments. This study integrated computational and in vitro approaches to identify promising phytocompounds with therapeutic potential. Staphopain B emerged as a target protein for its role in immune evasion, exhibiting stability during molecular dynamic simulation (MDS) with a root mean square deviation value of 2.376 Å. Screening 115 phytocompounds with antibacterial properties from the PubChem database identified 12 with drug-like properties, nine of which showed superior binding affinity to Staphopain B compared to a commercial antibiotic, doxycycline (-7.8 kcal mol-1). Notably, epoxyazadiradione and nimbolide displayed higher estimated free energy of binding scores (-7.91 and -7.93 kcal mol-1, respectively), indicating strong protein-ligand interactions. The root mean square fluctuation values for epoxyazadiradione and nimbolide were 1.097 and 1.034 Å, respectively, which was confirmed through MDS. Crude ethanolic extracts (100% and 70%) of neem (Azadirachta indica) leaves demonstrated narrow inhibition against the bacteria in comparison to doxycycline in the disc-diffusion assay. This study underscores the potential of phytocompounds as therapeutic agents against S. aureus; however, further in vitro experiments and testing of the phytocompounds in vivo are required.
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Affiliation(s)
| | | | - Nuhu Alam
- Department of Botany, Jahangirnagar University, Savar, Dhaka1342, Bangladesh
| | - Mahbubul Kabir Himel
- Department of Botany, Jahangirnagar University, Savar, Dhaka1342, Bangladesh
- Padma Bioresearch, Dhaka1342, Bangladesh
| | - Aparna Shil
- Department of Botany, Jahangirnagar University, Savar, Dhaka1342, Bangladesh
- Padma Bioresearch, Dhaka1342, Bangladesh
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4
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Girase R, Ahmad I, Oh JM, Mathew B, Vagolu SK, Tønjum T, Sriram D, Kumari J, Desai NC, Agrawal Y, Kim H, Patel HM. Design and Synthesis of the Linezolid Bioisosteres to Resolve the Serotonergic Toxicity Associated with Linezolid. ACS Med Chem Lett 2024; 15:924-937. [PMID: 38894926 PMCID: PMC11181505 DOI: 10.1021/acsmedchemlett.4c00114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 05/08/2024] [Accepted: 05/16/2024] [Indexed: 06/21/2024] Open
Abstract
Serotonergic toxicity due to MAO enzyme inhibition is a significant concern when using linezolid to treat MDR-TB. To address this issue, we designed linezolid bioisosteres with a modified acetamidomethyl side chain at the C-5 position of the oxazolidine ring to balance activity and reduce toxicity. Among these bioisosteres, R7 emerged as a promising candidate, demonstrating greater effectiveness against M. tuberculosis (Mtb) H37Rv cells with an MIC of 2.01 μM compared to linezolid (MIC = 2.31 μM). Bioisostere R7 also exhibited remarkable activity (MIC50) against drug-resistant Mtb clinical isolates, with values of 0.14 μM (INHR, inhA+), 0.53 μM (INHR, katG+), 0.24 μM (RIFR, rpoB+), and 0.92 μM (INHR INHR, MDR). Importantly, it was >6.52 times less toxic as compared to the linezolid toward the MAO-A and >64 times toward the MAO-B enzyme, signifying a substantial improvement in its drug safety profile.
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Affiliation(s)
- Rukaiyya
T. Girase
- Department
of Pharmaceutical Chemistry, R. C. Patel
Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra 4254, India
| | - Iqrar Ahmad
- Department
of Pharmaceutical Chemistry, R. C. Patel
Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra 4254, India
| | - Jong Min Oh
- Department
of Pharmacy, and Research Institute of Life Pharmaceutical Sciences, Sunchon National University, Suncheon 57922, Republic of Korea
| | - Bijo Mathew
- Department
of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, Kochi 690525, India
| | - Siva K. Vagolu
- Department
of Microbiology, University of Oslo, N-0316 Oslo, Norway
| | - Tone Tønjum
- Department
of Microbiology, University of Oslo, N-0316 Oslo, Norway
- Department
of Microbiology, Oslo University Hospital, N-0424 Oslo, Norway
| | - Dharmarajan Sriram
- Department
of Pharmacy, Birla Institute of Technology
and Science-Pilani, Hyderabad Campus, Jawahar Nagar, Shameerpet Mandal, R. R. District, Hyderabad 500078, India
| | - Jyothi Kumari
- Department
of Pharmacy, Birla Institute of Technology
and Science-Pilani, Hyderabad Campus, Jawahar Nagar, Shameerpet Mandal, R. R. District, Hyderabad 500078, India
| | - Nisheeth C. Desai
- Division
of Medicinal Chemistry, Department of Chemistry, (DST-FIST Sponsored)
Mahatma Gandhi Campus, Maharaja Krishnakumarsinhji
Bhavnagar University, Bhavnagar 364 002, India
| | - Yogesh Agrawal
- Department
of Pharmaceutical Chemistry, R. C. Patel
Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra 4254, India
| | - Hoon Kim
- Department
of Pharmacy, and Research Institute of Life Pharmaceutical Sciences, Sunchon National University, Suncheon 57922, Republic of Korea
| | - Harun M. Patel
- Department
of Pharmaceutical Chemistry, R. C. Patel
Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra 4254, India
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Halder SK, Ahmad I, Shathi JF, Mim MM, Hassan MR, Jewel MJI, Dey P, Islam MS, Patel H, Morshed MR, Shakil MS, Hossen MS. A Comprehensive Study to Unleash the Putative Inhibitors of Serotype2 of Dengue Virus: Insights from an In Silico Structure-Based Drug Discovery. Mol Biotechnol 2024; 66:612-625. [PMID: 36307631 PMCID: PMC9616416 DOI: 10.1007/s12033-022-00582-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 10/03/2022] [Indexed: 11/16/2022]
Abstract
Dengue fever is a mosquito-borne disease that claims the lives of millions of people around the world. A number of factors like disease's non-specific symptoms, increased viral mutation, growing antiviral drug resistance due to reduced susceptibility, unavailability of an effective vaccine for dengue, weak immunity against the virus, and many more are involved. Dengue belongs to the Flaviviridae family of viruses. The two species of the vector transmitting dengue are Aedes aegypti and Aedes albopictus, with the former one being dominant. Serotypes 2 of dengue fever are spread to the human body and cause severe illness. Recently, dengue has imposed an aggressive effect synergistically with the COVID-19 pandemic. As a result, we concentrated our efforts on finding a potential therapeutic. For this, we chose natural compounds to fight dengue fever, which is currently regarded as successful among many drug therapies. Following this, we started the in silico experiment with 922 plant extracts as lead compounds to fight serotype 2. In this study, we used SwissADME for analyzing ligand drug-likeness, pkCSM for designing an ADMET profile, Autodock vina 4.2 and Swissdock tools for molecular docking, and finally Desmond for molecular dynamics simulation. Ultimately 45 were found effective against the 2'O methyltransferase protein of serotype 2. CHEMBL376820 was found as possible therapeutic candidates for inhibiting methyltransferase protein in this thorough analysis. Nevertheless, more in vitro and in vivo research are required to substantiate their potential therapeutic efficacy.
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Affiliation(s)
- Sajal Kumar Halder
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka 1342 Bangladesh
- Division of Computer Aided Drug Design, BioAid, Mirpur, Dhaka, 1216 Bangladesh
| | - Iqrar Ahmad
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra 425405 India
| | - Jannatul Fardous Shathi
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka 1342 Bangladesh
- Division of Computer Aided Drug Design, BioAid, Mirpur, Dhaka, 1216 Bangladesh
| | - Maria Mulla Mim
- Department of Pharmacy, Jahangirnagar University, Savar, Dhaka 1342 Bangladesh
- Division of Computer Aided Drug Design, BioAid, Mirpur, Dhaka, 1216 Bangladesh
| | - Md Rakibul Hassan
- Department of Biochemistry, Gono Bishwabidyalay, Savar, Dhaka 1344 Bangladesh
- Division of Computer Aided Drug Design, BioAid, Mirpur, Dhaka, 1216 Bangladesh
| | - Md Johurul Islam Jewel
- Department of Biochemistry and Molecular Biology, Primeasia University, Banani, Dhaka 1213 Bangladesh
- Division of Computer Aided Drug Design, BioAid, Mirpur, Dhaka, 1216 Bangladesh
| | - Piyali Dey
- Department of Biochemistry and Molecular Biology, Primeasia University, Banani, Dhaka 1213 Bangladesh
- Division of Computer Aided Drug Design, BioAid, Mirpur, Dhaka, 1216 Bangladesh
| | - Md Sirajul Islam
- Department of Biochemistry and Molecular Biology, Primeasia University, Banani, Dhaka 1213 Bangladesh
- Division of Computer Aided Drug Design, BioAid, Mirpur, Dhaka, 1216 Bangladesh
| | - Harun Patel
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra 425405 India
| | - Md Reaz Morshed
- Department of Biochemistry and Molecular Biology, Noakhali Science and Technology University, Noakhali, 3814 Bangladesh
| | - Md Salman Shakil
- Department of Mathematics and Natural Sciences, Brac University, Dhaka, 1212 Bangladesh
- Division of Computer Aided Drug Design, BioAid, Mirpur, Dhaka, 1216 Bangladesh
| | - Md Sakib Hossen
- Department of Biochemistry and Molecular Biology, Primeasia University, Banani, Dhaka 1213 Bangladesh
- Division of Computer Aided Drug Design, BioAid, Mirpur, Dhaka, 1216 Bangladesh
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Sharma D, Gautam S, Srivastava N, Bisht D. In silico Screening of Food and Drug Administration-approved Compounds against Trehalose 2-sulfotransferase (Rv0295c) in Mycobacterium tuberculosis: Insights from Molecular Docking and Dynamics Simulations. Int J Mycobacteriol 2024; 13:73-82. [PMID: 38771283 DOI: 10.4103/ijmy.ijmy_20_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 02/25/2024] [Indexed: 05/22/2024] Open
Abstract
BACKGROUND Tuberculosis (TB) remains a prominent global health challenge, distinguished by substantial occurrences of infection and death. The upsurge of drug-resistant TB strains underscores the urgency to identify novel therapeutic targets and repurpose existing compounds. Rv0295c is a potentially druggable enzyme involved in cell wall biosynthesis and virulence. We evaluated the inhibitory activity of Food and Drug Administration (FDA)-approved compounds against Rv0295c of Mycobacterium tuberculosis, employing molecular docking, ADME evaluation, and dynamics simulations. METHODS The study screened 1800 FDA-approved compounds and selected the top five compounds with the highest docking scores. Following this, we subjected the initially screened ligands to ADME analysis based on their dock scores. In addition, the compound exhibited the highest binding affinity chosen for molecular dynamics (MD) simulation to investigate the dynamic behavior of the ligand-receptor complex. RESULTS Dihydroergotamine (CHEMBL1732) exhibited the highest binding affinity (-12.8 kcal/mol) for Rv0295c within this set of compounds. We evaluated the stability and binding modes of the complex over extended simulation trajectories. CONCLUSION Our in silico analysis demonstrates that FDA-approved drugs can serve as potential Rv0295c inhibitors through repurposing. The combination of molecular docking and MD simulation offers a comprehensive understanding of the interactions between ligands and the protein target, providing valuable guidance for further experimental validation. Identifying Rv0295c inhibitors may contribute to new anti-TB drugs.
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Affiliation(s)
- Devesh Sharma
- Department of Biochemistry, ICMR-National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, Uttar Pradesh, India
- School of Studies in Biochemistry, Jiwaji University, Gwalior, Madhya Pradesh, India
| | - Sakshi Gautam
- Department of Biochemistry, ICMR-National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, Uttar Pradesh, India
| | - Nalini Srivastava
- School of Studies in Biochemistry, Jiwaji University, Gwalior, Madhya Pradesh, India
| | - Deepa Bisht
- Department of Biochemistry, ICMR-National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, Uttar Pradesh, India
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Hossen MS, Hasan MN, Haque M, Al Arian T, Halder SK, Uddin MJ, Abdullah-Al-Mamun M, Shakil MS. Immunoinformatics-aided rational design of multiepitope-based peptide vaccine (MEBV) targeting human parainfluenza virus 3 (HPIV-3) stable proteins. J Genet Eng Biotechnol 2023; 21:162. [PMID: 38055114 DOI: 10.1186/s43141-023-00623-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 11/15/2023] [Indexed: 12/07/2023]
Abstract
BACKGROUND Human parainfluenza viruses (HPIVs) are common RNA viruses responsible for respiratory tract infections. Human parainfluenza virus 3 (HPIV-3) is particularly pathogenic, causing severe illnesses with no effective vaccine or therapy available. RESULTS The current study employed a systematic immunoinformatic/reverse vaccinology approach to design a multiple epitope-based peptide vaccine against HPIV-3 by analyzing the virus proteome. On the basis of a number of therapeutic features, all three stable and antigenic proteins with greater immunological relevance, namely matrix protein, hemagglutinin neuraminidase, and RNA-directed RNA polymerase L, were chosen for predicting and screening suitable T-cell and B-cell epitopes. All of our desired epitopes exhibited no homology with human proteins, greater population coverage (99.26%), and high conservancy among reported HPIV-3 isolates worldwide. All of the T- and B-cell epitopes are then joined by putative ligands, yielding a 478-amino acid-long final construct. Upon computational refinement, validation, and thorough screening, several programs rated our peptide vaccine as biophysically stable, antigenic, allergenic, and non-toxic in humans. The vaccine protein demonstrated sufficiently stable interaction as well as binding affinity with innate immune receptors TLR3, TLR4, and TLR8. Furthermore, codon optimization and virtual cloning of the vaccine sequence in a pET32a ( +) vector showed that it can be readily expressed in the bacterial system. CONCLUSION The in silico designed HPIV-3 vaccine demonstrated potential in evoking an effective immune response. This study paves the way for further preclinical and clinical evaluation of the vaccine, offering hope for a future solution to combat HPIV-3 infections.
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Affiliation(s)
- Md Sakib Hossen
- Department of Biochemistry and Molecular Biology, Primeasia University, Banani, Dhaka, 1213, Bangladesh.
- Division of Computer Aided Drug Design, BioAid, Mirpur, Dhaka, 1216, Bangladesh.
| | - Md Nazmul Hasan
- Division of Computer Aided Drug Design, BioAid, Mirpur, Dhaka, 1216, Bangladesh.
- Department of Biochemistry and Molecular Biology, Hajee Mohammad Danesh Science and Technology University, Dinajpur, 5200, Bangladesh.
| | - Munima Haque
- Biotechnology Program, Department of Mathematics and Natural Sciences (MNS), Brac University, kha-208, 1 Bir Uttam Rafiqul Islam Ave, Dhaka, 1212, Bangladesh
| | - Tawsif Al Arian
- Department of Pharmacy, Faculty of Biological Sciences, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh
| | - Sajal Kumar Halder
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh
| | - Md Jasim Uddin
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh
| | - M Abdullah-Al-Mamun
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh
| | - Md Salman Shakil
- Division of Computer Aided Drug Design, BioAid, Mirpur, Dhaka, 1216, Bangladesh
- Microbiology Program, Department of Mathematics and Natural Sciences (MNS), Brac University, 66 Mohakhali, Dhaka, 1212, Bangladesh
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8
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Halder SK, Sultana I, Shuvo MN, Shil A, Himel MK, Hasan MA, Shawan MMAK. In Silico Identification and Analysis of Potentially Bioactive Antiviral Phytochemicals against SARS-CoV-2: A Molecular Docking and Dynamics Simulation Approach. BIOMED RESEARCH INTERNATIONAL 2023; 2023:5469258. [PMID: 37214084 PMCID: PMC10195178 DOI: 10.1155/2023/5469258] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 02/07/2023] [Accepted: 04/05/2023] [Indexed: 05/24/2023]
Abstract
SARS-CoV-2, a deadly coronavirus sparked COVID-19 pandemic around the globe. With an increased mutation rate, this infectious agent is highly transmissible inducing an escalated rate of infections and death everywhere. Hence, the discovery of a viable antiviral therapy option is urgent. Computational approaches have offered a revolutionary framework to identify novel antimicrobial treatment regimens and allow a quicker, cost-effective, and productive conversion into the health center by evaluating preliminary and safety investigations. The primary purpose of this research was to find plausible plant-derived antiviral small molecules to halt the viral entrance into individuals by clogging the adherence of Spike protein with human ACE2 receptor and to suppress their genome replication by obstructing the activity of Nsp3 (Nonstructural protein 3) and 3CLpro (main protease). An in-house library of 1163 phytochemicals were selected from the NPASS and PubChem databases for downstream analysis. Preliminary analysis with SwissADME and pkCSM revealed 149 finest small molecules from the large dataset. Virtual screening using the molecular docking scoring and the MM-GBSA data analysis revealed that three candidate ligands CHEMBL503 (Lovastatin), CHEMBL490355 (Sulfuretin), and CHEMBL4216332 (Grayanoside A) successfully formed docked complex within the active site of human ACE2 receptor, Nsp3, and 3CLpro, respectively. Dual method molecular dynamics (MD) simulation and post-MD MM-GBSA further confirmed efficient binding and stable interaction between the ligands and target proteins. Furthermore, biological activity spectra and molecular target analysis revealed that all three preselected phytochemicals were biologically active and safe for human use. Throughout the adopted methodology, all three therapeutic candidates significantly outperformed the control drugs (Molnupiravir and Paxlovid). Finally, our research implies that these SARS-CoV-2 protein antagonists might be viable therapeutic options. At the same time, enough wet lab evaluations would be needed to ensure the therapeutic potency of the recommended drug candidates for SARS-CoV-2.
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Affiliation(s)
- Sajal Kumar Halder
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
| | - Ive Sultana
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
| | | | - Aparna Shil
- Department of Botany, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
| | | | - Md. Ashraful Hasan
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
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9
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Zampieri D, Fortuna S, Romano M, De Logu A, Cabiddu G, Sanna A, Mamolo MG. Synthesis, Biological Evaluation and Computational Studies of New Hydrazide Derivatives Containing 1,3,4-Oxadiazole as Antitubercular Agents. Int J Mol Sci 2022; 23:ijms232315295. [PMID: 36499618 PMCID: PMC9735621 DOI: 10.3390/ijms232315295] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/30/2022] [Accepted: 12/01/2022] [Indexed: 12/08/2022] Open
Abstract
To extend our screening for novel antimycobacterial molecules, we have designed, synthesized, and biologically evaluated a library of 14 new hydrazide derivatives containing 1,3,4-oxadiazole core. A variety of mycobacterial strains, including some drug-resistant strains, were tested for antimycobacterial activity. Among the compounds tested, five showed high antimycobacterial activity (MIC values of 8 μg/mL) against M. tuberculosis H37Ra attenuated strain, and two derivatives were effective (MIC of 4 µg/mL) against pyrazinamide-resistant strains. Furthermore, the novel compounds were tested against the fungal C. albicans strain, showing no antimycotic activity, and thus demonstrating a good selectivity profile. Notably, they also exhibited low cytotoxicity against human SH-SY5Y cells. The molecular modeling carried out suggested a plausible mechanism of action towards the active site of the InhA enzyme, which confirmed our hypothesis. In conclusion, the active compounds were predicted in silico for ADME properties, and all proved to be potentially orally absorbed in humans.
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Affiliation(s)
- Daniele Zampieri
- Department of Chemistry and Pharmaceutical Sciences, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
- Correspondence: ; Tel.: +39-040-5583677
| | - Sara Fortuna
- Italian Institute of Technology (IIT), Via E. Melen 83, 16152 Genova, Italy
| | - Maurizio Romano
- Department of Life Sciences, University of Trieste, Via Valerio 28/1, 34127 Trieste, Italy
| | - Alessandro De Logu
- Department of Life and Environmental Sciences, Section of Microbiology, University of Cagliari, 09042 Monserrato, Italy
| | - Gianluigi Cabiddu
- Department of Life and Environmental Sciences, Section of Microbiology, University of Cagliari, 09042 Monserrato, Italy
| | - Adriana Sanna
- Department of Public Health, Clinical and Molecular Medicine, University of Cagliari, 09042 Monserrato, Italy
| | - Maria Grazia Mamolo
- Department of Chemistry and Pharmaceutical Sciences, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
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Sukanya SH, Venkatesh T, Aditya Rao SJ, Pandith A. An efficient p-TSA catalyzed synthesis of some new substituted-(5-hydroxy-3-phenylisoxazol-4-yl)-1,3-dimethyl-1H-chromeno[2,3-d]pyrimidine-2,4(3H,5H)-dione/3,3-dimethyl-2H-xanthen-1(9H)-one scaffolds and evaluation of their pharmacological and computational investigations. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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11
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Younis MH, Mohammed ER, Mohamed AR, Abdel-Aziz MM, Georgey HH, Abdel Gawad NM. Design, Synthesis and Anti-Mycobacterium tuberculosis Evaluation of New Thiazolidin-4-one and Thiazolo[3,2-a][1,3,5]triazine Derivatives. Bioorg Chem 2022; 124:105807. [DOI: 10.1016/j.bioorg.2022.105807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 04/06/2022] [Accepted: 04/10/2022] [Indexed: 11/02/2022]
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Halder SK, Mim MM, Alif MMH, Shathi JF, Alam N, Shil A, Himel MK. Oxa-376 and Oxa-530 variants of β-lactamase: computational study uncovers potential therapeutic targets of Acinetobacter baumannii. RSC Adv 2022; 12:24319-24338. [PMID: 36128545 PMCID: PMC9412156 DOI: 10.1039/d2ra02939a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 08/17/2022] [Indexed: 11/21/2022] Open
Abstract
Antimicrobial resistance is a major global health crisis, resulting in thousands of deaths each year. Antibiotics' effectiveness against microorganisms deteriorates over time as multidrug resistance (MDR) develops, which is exacerbated by irregular antibiotic use, poor disease management, and the evasive nature of bacteria. The World Health Organization has recognized multidrug resistance as a critical public health concern, and Acinetobacter baumannii has been at the center of attention due to its ability to develop multidrug resistance (MDR). It generally produces carbapenem-hydrolyzing oxacillinase, which has been identified as the primary source of beta-lactam resistance in MDR bacteria. Recently, point mutations in A. baumannii have been identified as a key factor of multidrug resistance, making them a prime concern for researchers. The goal of the current work was to establish a unique way of finding multidrug-resistant variants and identify the most damaging mutations in the existing databases. We characterized the deleterious variants of oxacillinases using several computational tools. Following a thorough analysis, Oxa-376 and Oxa-530 were found to be more damaging when compared with the wild-type Oxa-51. The mutants' 3D structures were then prepared and refined with RaptorX, GalaxyRefine, and SAVES servers. Our research incorporates seven antimicrobial agents to illustrate the resistance capability of the variants of oxacillinase by evaluating binding affinity in Autodock-vina and Schrodinger software. RMSD, RMSF, Radius of gyration analysis, the solvent-accessible surface area (SASA), hydrogen bonding analysis and MM-GBSA from Molecular Dynamics Simulation revealed the dynamic nature and stability of wild-type and Oxa-376 and Oxa-530 variants. Our findings will benefit researchers looking for the deleterious mutations of Acinetobacter baumannii and new therapeutics to combat those variants. However, further studies are necessary to evaluate the mechanism of hydrolyzing activity and antibiotic resistance of these variants. Determining novel therapeutic targets of Acinetobacter baumannii. Deleterious variants, causing antibiotic resistance, were identified by molecular docking and molecular dynamics simulation suggesting new therapeutic targets Oxa-376 and Oxa-530.![]()
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Affiliation(s)
- Sajal Kumar Halder
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
- Research Assistant at Padma Bioresearch, Dhaka, Bangladesh
| | - Maria Mulla Mim
- Department of Pharmacy, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
| | - Md. Meharab Hassan Alif
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
| | - Jannatul Fardous Shathi
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
| | - Nuhu Alam
- Department of Botany, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
| | - Aparna Shil
- Department of Botany, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
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