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Wadapurkar RM, Sivaram A, Vyas R. Computational investigations into structure and function impact of novel mutations identified in targeted exons from ovarian cancer cell lines. J Biomol Struct Dyn 2024:1-15. [PMID: 38334284 DOI: 10.1080/07391102.2024.2310776] [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: 09/29/2023] [Accepted: 01/20/2024] [Indexed: 02/10/2024]
Abstract
The lack of sensitive and specific biomarkers for ovarian cancer leads to late stage diagnosis of the disease in a majority of the cases. Mutation accumulation is the basis for cancer progression, thus identifying mutations is an important step in the disease diagnosis. In the present study, a comprehensive analysis of fifteen Next Generation Sequencing samples from thirteen ovarian cancer cell lines was carried out for the identification of new mutations. The study revealed eight clinically significant novel mutations in six ovarian cancer oncogenes, viz. SMARCA4, ARID1A, PPP2R1A, CTNNB1, DICER1 and PIK3CA. In-depth computational analysis revealed that the mutations affected the structure of the proteins in terms of stability, solvent accessible surface area and molecular dynamics. Moreover, the mutations were present in functionally significant domains of the proteins, thereby adversely affecting the protein functionality. PPI network for SMARCA4, CTNNB1, DICER1, PIK3CA, PPP2R1A and ARID1A showed that these genes were involved in certain significant pathways affecting various hallmarks of cancer. For further validation, in vitro studies were performed that revealed hypermutability of the CTNNB1 gene. Through this study we have identified some key mutations and have analysed their structural and functional impact. The study establishes some key mutations, which can be potentially explored as biomarker and drug target.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rucha M Wadapurkar
- MIT School of Bioengineering Sciences & Research, MIT-ADT University, Pune, Maharashtra, India
| | - Aruna Sivaram
- MIT School of Bioengineering Sciences & Research, MIT-ADT University, Pune, Maharashtra, India
| | - Renu Vyas
- MIT School of Bioengineering Sciences & Research, MIT-ADT University, Pune, Maharashtra, India
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2
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Dey D, Kumar A. Unveiling the potential of recently FDA-approved drugs as quorum sensing inhibitors against P. Aeruginosa using high-performance computational techniques. J Biomol Struct Dyn 2024:1-18. [PMID: 38230441 DOI: 10.1080/07391102.2024.2304682] [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: 11/01/2023] [Accepted: 01/07/2024] [Indexed: 01/18/2024]
Abstract
Through cell-to-cell communication, activation of efflux pumps, formation of biofilms, and other mechanisms, pseudomonas aeruginosa's quorum sensing systems (QSS), notably the lasl/las-r system, contribute a vital role in the development of anti-microbial resistance (AMR). Identifying potential drugs against these targets could have significant implications for combating pseudomonal infections. The current study aims to identify promising recently FDA-approved drugs against lasl/las-r proteins. The ligands were selected from the FDA-approved drug lists of the last 5 years. Out of 202, 78 drugs were checked for interaction with lasl/las-r protein and 4 drugs revealed top binding conformations characterized by favorable energetic profiles within the active site of the las-r protein which were further assigned for 250-ns molecular dynamics (MD) simulation. The MD analysis confirmed the dynamical stability of brexanolone and oteseconazole with las-r protein. The root mean square deviation (RMSD), radius of gyration (Rg) and solvent-accessible surface area (SASA) analysis have indicated less deviation, more compactness of protein and less exposure of protein ligand complex to its surroundings as compared to the reference ligand-protein complex. The hydroxyl group in the oteseconazole whereas hydroxyl and ketone group in the brexanolone were responsible for hydrogen bonds with the active site residue of las r ptotein as indicated by ligand-protein contacts diagram. The binding energies per residue analysis revealed TYR-47 as the most contributing amino acid residue for interaction with oteseconazole and brexanolone. The identified drugs may be potential repurposing candidates against pseudomonal infections through inhibition of las-r protein.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Debanjan Dey
- Department of Pharmacology, Delhi Pharmaceutical Science, Research University (DPSRU), New Delhi, India
| | - Anoop Kumar
- Department of Pharmacology, Delhi Pharmaceutical Science, Research University (DPSRU), New Delhi, India
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3
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Kumar A, Novak J, Singh AK, Singh H, Thareja S, Pathak P, Grishina M, Verma A, Kumar P. Virtual screening, structure based pharmacophore mapping, and molecular simulation studies of pyrido[2,3-d]pyrimidines as selective thymidylate synthase inhibitors. J Biomol Struct Dyn 2023; 41:14197-14211. [PMID: 37154748 DOI: 10.1080/07391102.2023.2208205] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 02/04/2023] [Indexed: 05/10/2023]
Abstract
Human thymidylate synthase is the rate-limiting enzyme in the de novo synthesis of 2'-deoxythymidine-5'-monophosphate. dUMP (pyrimidine) and folate binding site hTS inhibitors showed resistance in colorectal cancer (CRC). In the present study, we have performed virtual screening of the pyrido[2,3-d]pyrimidine database, followed by binding free energy calculations, and pharmacophore mapping to design novel pyrido[2,3-d]pyrimidine derivatives to stabilize inactive confirmation of hTS. A library of 42 molecules was designed. Based on the molecular docking studies, four ligands (T36, T39, T40, and T13) were identified to have better interactions and docking scores with the catalytic sites [dUMP (pyrimidine) and folate binding sites] of hTS protein than standard drug, raltitrexed. To validate efficacy of the designed molecules, we performed molecular dynamics simulation studies at 1000 ns with principal component analysis and binding free energy calculations on the hTS protein, also drug likeness properties of all hits were in acceptable range. Compounds T36, T39, T40, and T13 interacted with the catalytic amino acid (Cys195), an essential amino acid for anticancer activity. The designed molecules stabilized the inactive conformation of hTS, resulting in the inhibition of hTS. The designed compounds will undergo synthesis and biological evaluation, which may yield selective, less toxic, and highly potent hTS inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Adarsh Kumar
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Ghudda, Bathinda, India
| | - Jurica Novak
- Department of Biotechnology, University of Rijeka, Rijeka, Croatia
- Center for Artificial Intelligence and Cyber security, University of Rijeka, Rijeka, Croatia
- Scientific and Educational Center 'Biomedical Technologies' School of Medical Biology, South Ural State University, Chelyabinsk, Russia
| | - Ankit Kumar Singh
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Ghudda, Bathinda, India
| | - Harshwardhan Singh
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Ghudda, Bathinda, India
| | - Suresh Thareja
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Ghudda, Bathinda, India
| | - Prateek Pathak
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
| | - Maria Grishina
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
| | - Amita Verma
- Bioorganic and Medicinal Chemistry Research Laboratory, Department of Pharmaceutical Sciences, Sam Higginbottom University of Agriculture Technology and Sciences, Prayagraj, India
| | - Pradeep Kumar
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Ghudda, Bathinda, India
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Venkatachalam S, Murlidharan N, Krishnan SR, Ramakrishnan C, Setshedi M, Pandian R, Barh D, Tiwari S, Azevedo V, Sayed Y, Gromiha MM. Understanding Drug Resistance of Wild-Type and L38HL Insertion Mutant of HIV-1 C Protease to Saquinavir. Genes (Basel) 2023; 14:533. [PMID: 36833460 PMCID: PMC9957153 DOI: 10.3390/genes14020533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 02/16/2023] [Accepted: 02/17/2023] [Indexed: 02/25/2023] Open
Abstract
Acquired immunodeficiency syndrome (AIDS) is one of the most challenging infectious diseases to treat on a global scale. Understanding the mechanisms underlying the development of drug resistance is necessary for novel therapeutics. HIV subtype C is known to harbor mutations at critical positions of HIV aspartic protease compared to HIV subtype B, which affects the binding affinity. Recently, a novel double-insertion mutation at codon 38 (L38HL) was characterized in HIV subtype C protease, whose effects on the interaction with protease inhibitors are hitherto unknown. In this study, the potential of L38HL double-insertion in HIV subtype C protease to induce a drug resistance phenotype towards the protease inhibitor, Saquinavir (SQV), was probed using various computational techniques, such as molecular dynamics simulations, binding free energy calculations, local conformational changes and principal component analysis. The results indicate that the L38HL mutation exhibits an increase in flexibility at the hinge and flap regions with a decrease in the binding affinity of SQV in comparison with wild-type HIV protease C. Further, we observed a wide opening at the binding site in the L38HL variant due to an alteration in flap dynamics, leading to a decrease in interactions with the binding site of the mutant protease. It is supported by an altered direction of motion of flap residues in the L38HL variant compared with the wild-type. These results provide deep insights into understanding the potential drug resistance phenotype in infected individuals.
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Affiliation(s)
- Sankaran Venkatachalam
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Nisha Murlidharan
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Sowmya R. Krishnan
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - C. Ramakrishnan
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Mpho Setshedi
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg 2000, South Africa
| | - Ramesh Pandian
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg 2000, South Africa
| | - Debmalya Barh
- Department of Genetics, Ecology, and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte 31270-901, Brazil
- Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur 721172, West Bengal, India
| | - Sandeep Tiwari
- Department of Genetics, Ecology, and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte 31270-901, Brazil
- Institute of Biology, Federal University of Bahia, Salvador, BA 40110-909, Brazil
- Institute of Health Sciences, Federal University of Bahia, Salvador, BA 40110-909, Brazil
| | - Vasco Azevedo
- Department of Genetics, Ecology, and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte 31270-901, Brazil
| | - Yasien Sayed
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg 2000, South Africa
| | - M. Michael Gromiha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
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Bayani F, Safaei Hashkavaei N, Karamian MR, Uskoković V, Sefidbakht Y. In silico design of a multi-epitope vaccine against the spike and the nucleocapsid proteins of the Omicron variant of SARS-CoV-2. J Biomol Struct Dyn 2023; 41:11748-11762. [PMID: 36703619 DOI: 10.1080/07391102.2023.2170470] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 12/22/2022] [Indexed: 01/28/2023]
Abstract
Computational studies can comprise an effective approach to treating and preventing viral infections. Since 2019, the world has been dealing with the outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The most important achievement in this short period of time in the effort to reduce morbidity and mortality was the production of vaccines and effective antiviral drugs. Although the virus has been significantly suppressed, it continues to evolve, spread, and evade the host's immune system. Recently, researchers have turned to immunoinformatics tools to reduce side effects and save the time and cost of traditional vaccine production methods. In the present study, an attempt has been made to design a multi-epitope vaccine with humoral and cellular immune response stimulation against the Omicron variant of SARS-CoV-2 by investigating new mutations in spike (S) and nucleocapsid (N) proteins. The population coverage of the vaccine was evaluated as appropriate compared to other studies. The results of molecular dynamics simulation and molecular mechanics/generalized Born surface area (MM/GBSA) calculations predict the stability and proper interaction of the vaccine with Toll-like receptor 4 (TLR-4) as an innate immune receptor. The results of the immune simulation show a significant increase in the coordinated response of IgM and IgG after the third injection of the vaccine. Also, in the continuation of the research, spike proteins from BA.4 and BA.5 lineages were screened by immunoinformatics filters and effective epitopes were suggested for vaccine design. Despite the high precision of computational studies, in-vivo and in-vitro research is needed for final confirmation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Fatemeh Bayani
- Protein Research Center, Shahid Beheshti University, Tehran, Iran
| | | | - Mohammad Reza Karamian
- Department of Cell and Molecular Biology, Faculty of Science, Kharazmi University, Tehran, Iran
| | - Vuk Uskoković
- TardigradeNano LLC, Irvine, CA, USA
- Department of Mechanical Engineering, San Diego State University, San Diego, CA, USA
| | - Yahya Sefidbakht
- Protein Research Center, Shahid Beheshti University, Tehran, Iran
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6
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Salari Z, Khosravi A, Pourkhandani E, Molaakbari E, Salarkia E, Keyhani A, Sharifi I, Tavakkoli H, Sohbati S, Dabiri S, Ren G, Shafie’ei M. The inhibitory effect of 6-gingerol and cisplatin on ovarian cancer and antitumor activity: In silico, in vitro, and in vivo. Front Oncol 2023; 13:1098429. [PMID: 36937441 PMCID: PMC10020515 DOI: 10.3389/fonc.2023.1098429] [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: 11/14/2022] [Accepted: 02/13/2023] [Indexed: 03/06/2023] Open
Abstract
Background Epithelial ovarian cancer is very common in women and causes hundreds of deaths per year worldwide. Chemotherapy drugs including cisplatin have adverse effects on patients' health. Complementary treatments and the use of herbal medicines can help improve the performance of medicine. 6-Gingerol is the major pharmacologically active component of ginger. In this study, we compared the effects of 6-gingerol, cisplatin, and their combination in apoptotic and angiogenetic activities in silico, in test tubes, and in in vivo assays against two ovarian cancer cell lines: OVCAR-3 and human umbilical vein endothelial cells (HUVECs). Methods The drug-treated cell lines were evaluated for their cytotoxicity, cell cycle, and apoptotic and angiogenetic gene expression changes. Results The proportion of apoptosis treated by 6-gingerol coupled with cisplatin was significantly high. In the evaluation of the cell cycle, the combination therapy also showed a significant promotion of a higher extent of the S sequence. The expression of p53 level, Caspase-8, Bax, and Apaf1 genes was amplified again with combination therapy. Conversely, in both cell lines, the cumulative drug concentrations reduced the expression of VEGF, FLT1, KDR, and Bcl-2 genes. Similarly, in the control group, combination treatment significantly decreased the expression of VEGF, FLT1, KDR, and Bcl-2 genes in comparison to cisplatin alone. Conclusions The findings of the present study demonstrated that the cisplatin and 6-gingerol combination is more effective in inducing apoptosis and suppressing the angiogenesis of ovarian cancer cells than using each drug alone.
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Affiliation(s)
- Zohreh Salari
- Obstetrics and Gynecology Center, Afzalipour School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Ahmad Khosravi
- Leishmaniasis Research Center, Kerman University of Medical Sciences, Kerman, Iran
- *Correspondence: Ahmad Khosravi, ; Elham Pourkhandani,
| | - Elham Pourkhandani
- Obstetrics and Gynecology Center, Afzalipour School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
- *Correspondence: Ahmad Khosravi, ; Elham Pourkhandani,
| | - Elaheh Molaakbari
- Department of Chemistry, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Ehsan Salarkia
- Leishmaniasis Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Alireza Keyhani
- Leishmaniasis Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Iraj Sharifi
- Leishmaniasis Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Hadi Tavakkoli
- Department of Clinical Science, School of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Samira Sohbati
- Obstetrics and Gynecology Center, Afzalipour School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Shahriar Dabiri
- Afzalipour School of Medicine and Pathology and Stem Cells Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Guogang Ren
- School of Engineering and Computer Science, University of Hertfordshire, Hatfield, United Kingdom
| | - Mohammad Shafie’ei
- Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran
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Thakare PP, Dakhane S, Shikh AN, Modak M, Patil A, Bobade VD, Mhaske PC. Design, Synthesis, Antimicrobial and Ergosterol Inhibition Activity of New 4-(Imidazo[1,2-a]Pyridin-2-yl)Quinoline Derivatives. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2021.1933107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Prashant P. Thakare
- Post-Graduate Department of Chemistry, S. P. Mandali’s Sir Parashurambhau College, Pune, Maharashtra, India
| | - Sagar Dakhane
- Department of Chemistry, Abasaheb Garware College, Pune, Maharashtra, India
| | - Abdullatif N. Shikh
- Post-Graduate Department of Chemistry, S. P. Mandali’s Sir Parashurambhau College, Pune, Maharashtra, India
- Department of Chemistry, Jijamata College of Science and Arts, Bhende, Ahmednagar, Pune, Maharashtra, India
| | - Manisha Modak
- Department of Zoology, S. P. Mandali’s Sir Parashurambhau College, Pune, Maharashtra, India
| | - Ashiwini Patil
- Department of Biotechnology, Viva College, Mumbai, Maharashtra, India
| | - Vivek D. Bobade
- Post-Graduate Department of Chemistry, H. P. T. Arts and R. Y. K. Science College, Nashik, Maharashtra, India
| | - Pravin C. Mhaske
- Post-Graduate Department of Chemistry, S. P. Mandali’s Sir Parashurambhau College, Pune, Maharashtra, India
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Mosallanejad S, Mahmoodi M, Tavakkoli H, Khosravi A, Salarkia E, Keyhani A, Dabiri S, Gozashti MH, Pardakhty A, Khodabandehloo H, Pourghadamyari H. Empagliflozin induces apoptotic-signaling pathway in embryonic vasculature: In vivo and in silico approaches via chick’s yolk sac membrane model. Front Pharmacol 2022; 13:970402. [PMID: 36120349 PMCID: PMC9474685 DOI: 10.3389/fphar.2022.970402] [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: 06/15/2022] [Accepted: 08/12/2022] [Indexed: 11/18/2022] Open
Abstract
The present investigation was conducted to evaluate the vascular-toxicity of empagliflozin (EMP) in embryonic vasculature. Firstly, the vascular-toxicity of the drug as well as its interaction with apoptotic regulator proteins was predicted via in silico approach. In the next step, the apoptotic-signaling pathway in embryonic vasculature was evaluated using a chick’s YSM model. In silico simulation confirmed vascular-toxicity of EMP. There was also an accurate affinity between EMP, Bax and Bcl-2 (−7.9 kcal/mol). Molecular dynamics assay revealed complex stability in the human body conditions. Furthermore, EMP is suggested to alter Bcl-2 more than BAX. Morphometric quantification of the vessels showed that the apoptotic activity of EMP in embryonic vasculature was related to a marked reduction in vessel area, vessel diameter and mean capillary area. Based on the qPCR and immunohistochemistry assays, enhanced expression level of BAX and reduced expression level of Bcl-2 confirmed apoptotic responses in the vessels of the YSM. We observed that induction of an apoptotic signal can cause the embryonic defect of the vascular system following EMP treatment. The acquired data also raised suspicions that alteration in apoptotic genes and proteins in the vasculature are two critical pathways in vascular-toxicity of EMP.
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Affiliation(s)
- Saeedeh Mosallanejad
- Department of Clinical Biochemistry, Afzalipour School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Mehdi Mahmoodi
- Department of Clinical Biochemistry, Afzalipour School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
- *Correspondence: Mehdi Mahmoodi, ; Hossein Pourghadamyari,
| | - Hadi Tavakkoli
- Department of Clinical Sciences, School of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Ahmad Khosravi
- Leishmaniasis Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Ehsan Salarkia
- Leishmaniasis Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Alireza Keyhani
- Leishmaniasis Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Shahriar Dabiri
- Afzalipour School of Medicine, Pathology and Stem Cell Research Center, Kerman University of Medical Science, Kerman, Iran
| | - Mohammad Hossein Gozashti
- Endocrinology and Metabolism Research Center, Institute of Basic and Clinical Physiology Sciences, Kerman University of Medical Sciences, Kerman, Iran
| | - Abbas Pardakhty
- Pharmaceutics Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Hadi Khodabandehloo
- Department of Clinical Biochemistry, School of Medicine Zanjan University of Medical Sciences, Zanjan, Iran
| | - Hossein Pourghadamyari
- Department of Clinical Biochemistry, Afzalipour School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
- Gastroenterology and Hepatology Research Center, Institute of Basic and Clinical Physiology Sciences, Kerman University of Medical Sciences, Kerman, Iran
- *Correspondence: Mehdi Mahmoodi, ; Hossein Pourghadamyari,
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Abisha W, Dhas DA, Balachandran S, Joe IH. Molecular Structure, Spectroscopic Elucidation (FT-IR, FT-Raman, UV-Visible and NMR) with NBO, ELF, LOL, RDG, Fukui, Drug Likeness and Molecular Docking Analysis on Dimethomorph. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2083195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- W. Abisha
- Department of Physics & Research Centre, Nesamony Memorial Christian College, Marthandam, Tamilnadu, India
- Department of Physics, Manonmaniam Sundaranar University Abishekapatti, Tirunelveli, India
| | - D. Arul Dhas
- Department of Physics & Research Centre, Nesamony Memorial Christian College, Marthandam, Tamilnadu, India
- Department of Physics, Manonmaniam Sundaranar University Abishekapatti, Tirunelveli, India
| | | | - I. Hubert Joe
- Department of Physics, Centre for Molecular and Biophysics Research, Mar Ivanios College, Thiruvanathapuram, India
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10
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Potential Action Mechanism and Inhibition Efficacy of Morinda citrifolia Essential Oil and Octanoic Acid against Stagonosporopsis cucurbitacearum Infestations. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27165173. [PMID: 36014413 PMCID: PMC9414982 DOI: 10.3390/molecules27165173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 08/02/2022] [Accepted: 08/09/2022] [Indexed: 11/16/2022]
Abstract
The use of plant-based products has been shown to efficiently inhibit fungi-mediated diseases in agricultural crops. Here, we extracted and evaluated the composition of noni, Morinda citrifolia L., essential oil and assessed its activities against Stagonosporopsis cucurbitacearum in Cucumis melo L. Using in silico molecular approaches, potential interactions between the essential oil major components and S. cucurbitacearum tyrosine-tRNA ligase were predicted. Finally, we also measured the potential interference of plant physiology (the stomatal conductance and net photosynthesis) mediated by the application of the M. citrifolia essential oil. Chromatographic analysis revealed that octanoic acid (75.8%), hexanoic acid (12.8%), and isobutyl pent-4-enyl carbonate (3.1%) were the major essential oil compounds. Octanoic acid and noni essential oil, when used as preventive measures, reduce fungal mycelial growth at a concentration of 5 mg/mL without causing significant damage to the treated leaves, which reinforces their efficacies as preventive tools against S. cucurbitacearum. Molecular docking analyses predicted very stable interactions between the major essential oil constituents and S. cucurbitacearum tyrosine-tRNA ligase, suggesting the interference of these plant-based molecules upon enzyme activation. Octanoic acid and M. citrifolia essential oil at concentrations of 20 mg/mL decreased the stomatal conductance and net photosynthesis rate of melon plants, resulting in robust phytotoxicity. Collectively, our findings indicated that despite the phytotoxicity risks at higher concentrations, M. citrifolia essential oil and octanoic acid, have potential as alternative tools for the integrative management of S. cucurbitacearum.
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Waseem M, Thakur JK, Subbarao N. Prediction of novel and potent inhibitors of lanosterol 14-α demethylase. J Biomol Struct Dyn 2022:1-13. [DOI: 10.1080/07391102.2022.2096116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Mohd Waseem
- School of computational and integrative sciences, Jawaharlal Nehru University, New Delhi, India
| | - Jitendra K. Thakur
- Plant Transcription Regulation Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
- Plant Mediator Lab, National Institute of Plant Genome Research, New Delhi, India
| | - Naidu Subbarao
- School of computational and integrative sciences, Jawaharlal Nehru University, New Delhi, India
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12
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Kulkarni PS, Sarda SR, Khandebharad AU, Farooqui M, Agrawal BR. Pyrazole Linked-1,2,4-Oxadiazole Derivatives as Potential Pharmacological Agent: Design, Synthesis and Antimicrobial Study. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2072914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
| | - Swapnil R. Sarda
- Department of Chemistry, J. E. S. College, Jalna, Maharashtra, India
| | | | - Mazahar Farooqui
- Department of Chemistry, Maulana Azad College, Aurangabad, Maharashtra, India
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13
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Verma AK, Majid A, Hossain MS, Ahmed SKF, Ashid M, Bhojiya AA, Upadhyay SK, Vishvakarma NK, Alam M. Identification of 1, 2, 4-Triazine and Its Derivatives Against Lanosterol 14-Demethylase (CYP51) Property of Candida albicans: Influence on the Development of New Antifungal Therapeutic Strategies. FRONTIERS IN MEDICAL TECHNOLOGY 2022; 4:845322. [PMID: 35419560 PMCID: PMC8996309 DOI: 10.3389/fmedt.2022.845322] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 02/25/2022] [Indexed: 01/09/2023] Open
Abstract
This research aims to find out whether the 1, 2, 4-triazine and its derivatives have antifungal effects and can protect humans from infection with Candida albicans. Molecular docking and molecular dynamic simulation are widely used in modern drug design to target a particular protein with a ligand. We are interested in using molecular docking and molecular dynamics modeling to investigate the interaction between the derivatives of 1, 2, 4-triazine with enzyme Lanosterol 14-demethylase (CYP51) of Candida albicans. The inhibition of Candida albicans CYP51 is the main goal of our research. The 1, 2, 4-triazine and its derivatives have been docked to the CYP51 enzyme, which is involved in Candida albicans Multidrug Drug Resistance (MDR). Autodock tools were used to identify the binding affinities of molecules against the target proteins. Compared to conventional fluconazole, the molecular docking results indicated that each drug has a high binding affinity for CYP51 proteins and forms unbound interactions and hydrogen bonds with their active residues and surrounding allosteric residues. The docking contacts were made using a 10 ns MD simulation with nine molecules. RMSD, RMSF, hydrogen bonds, and the Rg all confirm these conclusions. In addition, these compounds were expected to have a favorable pharmacological profile and low toxicity. The compounds are being offered as scaffolds for the development of new antifungal drugs and as candidates for future in vitro testing.
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Affiliation(s)
- Abhishek Kumar Verma
- Department of Biosciences, Manipal University, Jaipur, India
- *Correspondence: Abhishek Kumar Verma
| | - Aarfah Majid
- Department of Chemistry, Faculty of Science and Technology, Mewar University, Chittorgarh, India
| | - Md. Shahadat Hossain
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - SK. Faisal Ahmed
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Mohammad Ashid
- Department of Chemistry, Faculty of Science and Technology, Mewar University, Chittorgarh, India
| | - Ali Asger Bhojiya
- Department of Science, U.S. Ostwal Science, Arts & Commerce College, Chittorgarh, India
- Ali Asger Bhojiya
| | - Sudhir K. Upadhyay
- Department of Environmental Science, V.B.S. Purvanchal University, Jaunpur, India
| | | | - Mudassir Alam
- Department of Zoology, Aligarh Muslim University, Aligarh, India
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14
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Preparation, Antimicrobial Activity and Docking Study of Vanadium Mixed Ligand Complexes Containing 4-Amino-5-hydrazinyl-4H-1,2,4-triazole-3-thiol and Aminophenol Derivatives. Processes (Basel) 2021. [DOI: 10.3390/pr9061008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The synthesis of mixed-ligand complexes is considered an important strategy for developing new metal complexes of enhanced biological activity. This paper presents the synthesis, characterization, in vitro antimicrobial assessment, and theoretical molecular docking evaluation for synthesized oxidovanadium (V) complexes. The proposed structures of the synthesized compounds were proved using elemental and different spectroscopic analysis. The antimicrobial tests showed moderate activity of the compounds against the Gram-positive bacterial strains and the fungal yeast, whereas no activity was observed against the Gram-negative bacterial strains. The performance of density functional theory (DFT) was conducted to study the interaction mode of the targeted compounds with the biological system. Calculating the quantitative structure-activity relationship (QSPR) was performed depending on optimization geometries, frontier molecular orbitals (FMOs), and chemical reactivities for synthesized compounds. The molecular electrostatic potentials (MEPs) that were plotted link the interaction manner of synthesized compounds with the receptor. The molecular docking evaluation revealed that the examined compounds may possess potential antibacterial activity.
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15
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Naglah AM, Moustafa GO, Elhenawy AA, Mounier MM, El-Sayed H, Al-Omar MA, Almehizia AA, Bhat MA. N α-1, 3-Benzenedicarbonyl-Bis-(Amino Acid) and Dipeptide Candidates: Synthesis, Cytotoxic, Antimicrobial and Molecular Docking Investigation. DRUG DESIGN DEVELOPMENT AND THERAPY 2021; 15:1315-1332. [PMID: 33790542 PMCID: PMC8006965 DOI: 10.2147/dddt.s276504] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 01/23/2021] [Indexed: 12/14/2022]
Abstract
Purpose The objective of our work was to prepare a potent and safe antimicrobial and anticancer agents, through synthesis of several peptides and examine their biological activities, namely as, cytotoxically potent and antimicrobial and antifungal agents. Introduction Multidrug-resistant microbial strains have arisen against all antibiotics in clinical use. Infections caused by these bacteria threaten global public health and are associated with high mortality rates. Methods The main backbone structure for the novel synthesized linear peptide is Nα-1, 3-benzenedicarbonyl-bis-(Amino acids)-X, (3–11). A computational docking study against DNA gyrase was performed to formulate a mode of action of the small compounds as antimicrobial agents. Results The peptide-bearing methionine-ester (4) exhibited potent antimicrobial activity compared to the other synthesized compounds, while, peptide (8), which had methionine-hydrazide fragment was the most potent as antifungal agent against Aspergillus niger with 100% inhibition percent. Compounds (6 and 7) showed the highest potency against breast human tumor cell line “MCF-7” with 95.1% and 79.8% of cell inhibition, respectively. The nine compounds possessed weak to moderate antiproliferative effect over colon tumor cell line. The docking results suggest good fitting through different hydrogen bond interactions with the protein residues. In silico ADMET study also evaluated and suggested that these compounds had promising oral bioavailability features. Conclusion The tested compounds need further modification to have significant antimicrobial and antitumor efficacy compared to the reference drugs.
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Affiliation(s)
- Ahmed M Naglah
- Department of Pharmaceutical Chemistry, Drug Exploration & Development Chair (DEDC), College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia.,Peptide Chemistry Department, Chemical Industries Research Division, National Research Centre, Cairo, Egypt
| | - Gaber O Moustafa
- Peptide Chemistry Department, Chemical Industries Research Division, National Research Centre, Cairo, Egypt
| | - Ahmed A Elhenawy
- Chemistry Department, Faculty of Science, Al-Azhar University (Boys'Branch), Cairo, Egypt.,Chemistry Department, Faculty of Science, Albaha University, Al Baha, Saudi Arabia
| | - Marwa M Mounier
- Pharmacognosy Department, Pharmaceutical and Drug Industries Research Division, National Research Centre, Giza, Egypt
| | - Heba El-Sayed
- Botany and Microbiology Department, Faculty of Science, Helwan University, Helwan, Egypt
| | - Mohamed A Al-Omar
- Department of Pharmaceutical Chemistry, Drug Exploration & Development Chair (DEDC), College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Abdulrahman A Almehizia
- Department of Pharmaceutical Chemistry, Drug Exploration & Development Chair (DEDC), College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia.,Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Mashooq A Bhat
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
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16
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Dong HH, Wang YH, Peng XM, Zhou HY, Zhao F, Jiang YY, Zhang DZ, Jin YS. Synergistic antifungal effects of curcumin derivatives as fungal biofilm inhibitors with fluconazole. Chem Biol Drug Des 2021; 97:1079-1088. [PMID: 33506609 DOI: 10.1111/cbdd.13827] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 01/10/2021] [Indexed: 11/28/2022]
Abstract
Lack of novel antifungal agents and severe drug resistance has led to high incidence and associated mortality of invasive fungal infections. To tackle the challenges, novel antifungal agents with anti-resistant potency are highly desirable. Thus, derivatives of curcumin were synthesized to restore the effectiveness of fluconazole (FLC) against FLC-resistant Candida spp. and structure-activity relationships were then discussed. Some novel derivatives showed promising features as novel antifungal lead compounds. Of them, compound 4 showed good alone or synergistic antifungal activity against FLC-resistant Candida spp. Moreover, compound 4 was proven as a potent inhibitor of Candida albicans biofilm formation and yeast-to-hypha morphological transition whether used alone or in combination with FLC, which was further confirmed by the inhibitory effect on cellular surface hydrophobicity of C. albicans. Compound 4 also inhibits intracellular ATP production of C. albicans and disrupts membrane permeability of C. albicans when used in combination with FLC. The results highlighted the potential of curcumin derivatives to overcome fluconazole-related and biofilm-related drug resistance.
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Affiliation(s)
- Huai-Huai Dong
- School of Pharmacy, Second Military Medical University, Shanghai, China.,Department of Pharmacy, The Air Force Hospital of Northern Theater PLA, Shenyang, China
| | - Yuan-Hua Wang
- Yue-yang Hospital of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xue-Mi Peng
- School of Pharmacy, Second Military Medical University, Shanghai, China
| | - He-Yang Zhou
- School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Fei Zhao
- School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Yuan-Ying Jiang
- Department of Pharmacology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Da-Zhi Zhang
- School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Yong-Sheng Jin
- School of Pharmacy, Second Military Medical University, Shanghai, China
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17
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Tanhaian A, Mohammadi E, Vakili-Ghartavol R, Saberi MR, Mirzayi M, Jaafari MR. In silico and In vitro Investigation of a Likely Pathway for Anti-Cancerous Effect of Thrombocidin-1 as a Novel Anticancer Peptide. Protein Pept Lett 2021; 27:751-762. [PMID: 32072885 DOI: 10.2174/0929866527666200219115129] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 11/22/2019] [Accepted: 12/16/2019] [Indexed: 02/01/2023]
Abstract
BACKGROUND Antimicrobial and antifungal activities of Thrombocidin-1 (TC-1) is shown previously, however,.the anti-cancerous feature of this peptide is still uncovered. OBJECTIVE The objective is to evaluate anti-cancerous feature of recombinant TC-1. METHODS In this study, based on the significant similarity of rTC-1 and IL-8 in case of coding sequence, tertiary structure, and also docking and molecular dynamic simulation (MD) results with CXCR1, a receptor which has positive correlation with different cancers, a likely pathway for anticancerous effect of rTC-1 was proposed. In addition, the coding sequence of TC-1+6xhistidine (rTC-1) was inserted into the pET22b(+) vector and cloned and expressed by E. coli BL21 and finally purified through nickel affinity column. Afterward, the retrieved rTC-1 was used in MTT assay against mouse colon adenocarcinoma, hepatocellular carcinoma, chondrosarcoma, mouse melanoma, and breast adenocarcinoma cell lines to investigate its probable anticancer application. RESULTS Docking and MD simulation results showed that rTC-1 and IL-8 share almost the same residues in the interaction with CXCR1 receptor. Besides, the stability of the rTC-1_CXCR11-38 complex was shown during 100ns MD simulation. In addition, the successful expression and purification of rTC-1 depict an 8kD peptide. The IC50 results of MTT assay revealed that rTC-1 has cytotoxic effect on C26-A and SW1353 cancerous cell lines. CONCLUSION Therefore, apart from probable anti-cancerous effect of rTC-1 on C26-A and SW1353 cell lines, this peptide may be able to mimic the anti-cancerous pathway of IL-8.
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Affiliation(s)
- Abbas Tanhaian
- School of Medicine, Shahrood University of Medical Science, Shahrood, Iran
| | - Elyas Mohammadi
- Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Roghayyeh Vakili-Ghartavol
- Department of Medical Nanotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Saberi
- Medical Chemistry Department, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mehdi Mirzayi
- School of Medicine, Shahrood University of Medical Science, Shahrood, Iran
| | - Mahmoud Reza Jaafari
- Nanotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
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18
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Deshapriya US, Dinuka DLS, Ratnaweera PB, Ratnaweera CN. In silico study for prediction of novel bioactivities of the endophytic fungal alkaloid, mycoleptodiscin B for human targets. J Mol Graph Model 2020; 102:107767. [PMID: 33130394 DOI: 10.1016/j.jmgm.2020.107767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/23/2020] [Accepted: 09/28/2020] [Indexed: 11/28/2022]
Abstract
Mycoleptodiscin B is a natural product extracted from the endophytic fungus Mycoleptodiscus sp. found in Sri Lanka and Panama with experimentally unexplored activities for human targets. In this study, a computational methodology was applied to determine druggable targets of mycoleptodiscin B. According to the computational toxicity and pharmacokinetics assessment, mycoleptodiscin B was proven to be a suitable drug candidate. Druggable targets for this compound, aromatase, acidic plasma glycoprotein and androgen receptor, were predicted using reverse docking. A two-step validation of those targets was performed using conventional molecular docking and molecular dynamic (MD) simulations, resulting in aromatase being determined as the potential therapeutic target. Based on molecular mechanics/Generalized Born Surface Area (GBSA) free energies and ligand stability inside the active site cavity during its 120 ns MD run, it can be concluded that mycoleptodiscin B is a potent aromatase inhibitor and could be subjected to further in vitro and in vivo experiments in the drug development pipeline. Consequently, natural product chemists can quickly identify the hidden medicinal properties of their miracle compounds using the computational approach applied in this research.
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Affiliation(s)
- Uthpala S Deshapriya
- College of Chemical Sciences, Institute of Chemistry Ceylon, Rajagiriya, Sri Lanka; Faculty of Medicine, University of Colombo, Colombo, Sri Lanka
| | - D L Senal Dinuka
- College of Chemical Sciences, Institute of Chemistry Ceylon, Rajagiriya, Sri Lanka; Department of Chemistry, Mississippi State University, Mississippi State, USA
| | - Pamoda B Ratnaweera
- Department of Science and Technology, Faculty of Applied Sciences, Uva Wellassa University, Badulla, Sri Lanka
| | - Chinthaka N Ratnaweera
- College of Chemical Sciences, Institute of Chemistry Ceylon, Rajagiriya, Sri Lanka; Department of Chemistry, University of Ruhuna, Matara, Sri Lanka.
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19
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Chagovets VV, Starodubtseva NL, Frankevich VE. Complexes of fluconazole with alanine, lysine and threonine: mass spectrometry and theoretical modeling. BULLETIN OF RUSSIAN STATE MEDICAL UNIVERSITY 2020. [DOI: 10.24075/brsmu.2020.048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Investigation of the triazole-derived drugs action mechanisms and understanding of their affinity and specificity molecular basis may contribute to the new drugs development. The study was aimed to investigate the triazoles class representative (fluconazole) complexes with amino acids using mass spectrometry, molecular dynamics and ab initio quantum chemistry calculations. During the experimental study, the fluconazole, alanine, lysine and threonine solutions were analyzed by electrospray ionization mass spectrometry and tandem mass spectrometry. The molecular dynamics modeling of the fluconazole–amino acid complexes was performed using the CHARMM force field. The quantum chemistry calculations of the complexes structure and energy parameters were carried out using the density-functional theory by B3LYP calculations (3-21G and 6-311++G** basis sets). Mass spectra indicated that fluconazole formed stable complexes with amino acids in the 1 : 1 stoichiometric ratio. In accordance with the tandem mass spectrometry with varying fluconazole–amino acid associates ion fragmentation energy, the following sequence was obtained: [Fluc + Ala + H]+ < [Fluc + Lys + H]+ < [Fluc + Thr + H]+. The fluconazole–amino acid interaction energy values resulting from the quantum chemistry calculations formed the sequence similar to that obtained by experiment. Thus, as seen in the case of fluconazole–amino acid complexes, it is possible to combine the experimental mass spectrometry studies with quantum chemical modeling for the complexes properties assessment.
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Affiliation(s)
- VV Chagovets
- National Medical Research Center for Obstetrics, Gynecology and Perinatology named after Academician V. I. Kulakov, Moscow, Russia
| | - NL Starodubtseva
- National Medical Research Center for Obstetrics, Gynecology and Perinatology named after Academician V. I. Kulakov, Moscow, Russia
| | - VE Frankevich
- National Medical Research Center for Obstetrics, Gynecology and Perinatology named after Academician V. I. Kulakov, Moscow, Russia
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20
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Dwivedi VD, Arya A, Sharma T, Sharma S, Patil SA, Gupta VK. Computational investigation of phytomolecules as resuscitation-promoting factor B (RpfB) inhibitors for clinical suppression of Mycobacterium tuberculosis dormancy reactivation. INFECTION GENETICS AND EVOLUTION 2020; 83:104356. [PMID: 32438079 DOI: 10.1016/j.meegid.2020.104356] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 05/03/2020] [Accepted: 05/06/2020] [Indexed: 01/03/2023]
Abstract
Among the various strategies of curbing tuberculosis, suppression of Mycobacterium tuberculosis (Mtb) is a primary goal of the WHO to stop its infection, which is further strengthened by the presence of a massive reservoir of latently infected individuals. Several efforts have been made to explore potential candidates, including drug-repurposing, phytomolecules evaluation, and de novo designs. Compared to other strategies, investigation of phytomolecules with known experimental evidence represents a highly cost-effective and less time-consuming approach. Interestingly, some of the phytomolecules, previously known to show anti-tuberculosis effects, are known. While, these compounds have not yet been tested for their additional abilities to interact with resuscitation-promoting factor B (RpfB), an essential protein involved in revoking of Mtb dormancy. We, therefore, performed an initial computational study to evaluate the binding affinity of 38 phytomolecules to select the most effective ligands against RpfB. The studies were carried out using AutoDock and associated tools for static interaction analysis, while molecular dynamics (MD) simulations were performed to examine the stability of predicted protein-ligand complexes using the Desmond MD package. As an outcome of this study, we have reported four potential compounds, viz. diospyrin, 2'-Nortiliacorinine, 5,4'-dihydroxy-3,7,8,3'-tetramethoxyflavone, and tiliacorine which showed a putative binding affinity with significant intermolecular interactions, docking energy of -8.0 kcal/mol or higher, and vital complex stability (~2.4 Å RMSD) during 100 ns MD simulation. The findings of this study indicated that phytomolecules are capable to efficiently inhibit the RpfB, which is vital for reactivation of dormant Mtb. Characterization of the molecular targets for hits with intriguingly selective activity against dormant Mtb would be helpful to elucidate the essential mechanisms underlying the survival of dormant Mtb during latent infections.
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Affiliation(s)
- Vivek Dhar Dwivedi
- Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India.
| | - Aditya Arya
- Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India.
| | - Tanuj Sharma
- Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India.
| | - Shweta Sharma
- ICMR-National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Tajganj, Agra 282004, India.
| | - Shripad A Patil
- ICMR-National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Tajganj, Agra 282004, India.
| | - Vivek Kumar Gupta
- ICMR-National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Tajganj, Agra 282004, India.
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21
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Farhadi Z, Farhadi T, Hashemian SM. Virtual screening for potential inhibitors of β(1,3)-D-glucan synthase as drug candidates against fungal cell wall. J Drug Assess 2020; 9:52-59. [PMID: 32284908 PMCID: PMC7144292 DOI: 10.1080/21556660.2020.1734010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 02/07/2020] [Indexed: 01/17/2023] Open
Abstract
Background To enhance the outcome in patients with invasive candidiasis, initiation of an efficient antifungal treatment in a suitable dosage is necessary. Echinocandins (e.g. caspofungin) inhibit the enzyme β(1,3)-D-glucan synthase of the fungal cell wall. Compared to azoles and other antifungal agents, echinocandins have lower adverse effects and toxicity in humans. Echinocandins are available in injectable (intravenous) form. Methods In this study, to identify the novel oral drug-like compounds that affect the fungal cell wall, downloaded oral drug-like compounds from the ZINC database were processed with a virtual screening procedure. The docking free energies were calculated and compared with the known inhibitor caspofungin. Four molecules were selected as the most potent ligands and subjected to hydrogen bonds analysis. Results Considering the hydrogen bond analysis, two compounds (ZINC71336662 and ZINC40910772) were predicted to better interact with the active site of β(1,3)-D-glucan synthase compared with caspofungin. Conclusion The introduced compound in this study may be valuable to analyze experimentally as a novel oral drug candidate targeting fungal cell walls.
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Affiliation(s)
- Zinat Farhadi
- Chronic Respiratory Diseases Research Center (CRDRC), National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Behavioral Disease Counseling Center, Marvdasht Health Center, Shiraz University of Medical Sciences, Shiraz, Iran.,Department of Microbiology, Shiraz Branch, Islamic Azad University, Shiraz, Iran
| | - Tayebeh Farhadi
- Chronic Respiratory Diseases Research Center (CRDRC), National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Seyed MohammadReza Hashemian
- Chronic Respiratory Diseases Research Center (CRDRC), National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Critical Care Department, Farhikhtegan Hospital, Tehran Medical Branch, Islamic Azad University, Tehran, Iran
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22
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Navyashree V, Kant K, Kumar A. Natural chemical entities from Arisaema genus might be a promising break-through against Japanese encephalitis virus infection: a molecular docking and dynamics approach. J Biomol Struct Dyn 2020; 39:1404-1416. [PMID: 32072856 DOI: 10.1080/07391102.2020.1731603] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- V. Navyashree
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Raebareli, Uttar Pradesh, India
| | - Kamal Kant
- Department of Pharmaceutical Chemistry, Birla Institute of Technology (B.I.T) Mesra, Ranchi, Jharkhand, India
| | - Anoop Kumar
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Raebareli, Uttar Pradesh, India
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23
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Rana R, Sharma R, Kumar A. Repurposing of Existing Statin Drugs for Treatment of Microbial Infections: How Much Promising? Infect Disord Drug Targets 2020; 19:224-237. [PMID: 30081793 DOI: 10.2174/1871526518666180806123230] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Revised: 05/20/2018] [Accepted: 07/23/2018] [Indexed: 01/27/2023]
Abstract
Today's microbial infections' resistance to approved drugs, the emergence of new infectious diseases and lack of vaccines, create a huge threat to human health. Thus, there is an urgent need to create novel antimicrobial agents, but the high cost and prolonged timeline of novel drug discovery and development is the major barrier to make new drugs. Therefore, there is a need for specific cost effective approaches in order to identify new drugs for the treatment of various microbial infections. Drug repurposition is an alternative technique to find existing clinically approved drugs for other indications. This approach may enhance the portfolio of Pharmaceutical companies by reducing the time and money required for the development of new chemical entity. In literature, various studies have reported some encouraging results regarding the antimicrobial use of existing statin drugs. Further, some clinical studies have also shown the protective effect of statin drugs in reduction of the morbidity and mortality due to many infectious diseases but complete understanding is still lacking. Thus, there is a need for better understanding of the use of statin drugs, especially in the context of antimicrobial effects. In this review, we try to summarize the use of statin drugs in various infectious diseases and their proposed antimicrobial mechanism of action. Further, current challenges and future perspectives of repurposition of statin drugs as antimicrobial agents have also been discussed.
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Affiliation(s)
- Ritika Rana
- Department of Pharmacology, Indo-Soviet Friendship Pharmacy College (ISFCP), Moga, Punjab, India
| | - Ruchika Sharma
- Department of Biotechnology, Indo-Soviet Friendship Institute of Professional Studies (ISFIPS), Moga, Punjab, India
| | - Anoop Kumar
- Department of Pharmacology, Indo-Soviet Friendship Pharmacy College (ISFCP), Moga, Punjab, India
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24
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Kant K, Rawat R, Bhati V, Bhosale S, Sharma D, Banerjee S, Kumar A. Computational identification of natural product leads that inhibit mast cell chymase: an exclusive plausible treatment for Japanese encephalitis. J Biomol Struct Dyn 2020; 39:1203-1212. [PMID: 32036760 DOI: 10.1080/07391102.2020.1726820] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kamal Kant
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER), Guwahati, Assam, India
- National Centre for Pharmacoengineering, National Institute of Pharmaceutical Education and Research (NIPER), Guwahati, Assam, India
| | - Ravi Rawat
- Department of Pharmaceutical Sciences and Technology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India
| | - Vipin Bhati
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Raebareli, Uttar Pradesh, India
| | - Shailesh Bhosale
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Raebareli, Uttar Pradesh, India
| | - Dalchand Sharma
- Regional Centre for Biotechnology, Faridabad, Haryana, India
| | - Subham Banerjee
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER), Guwahati, Assam, India
- National Centre for Pharmacoengineering, National Institute of Pharmaceutical Education and Research (NIPER), Guwahati, Assam, India
| | - Anoop Kumar
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Raebareli, Uttar Pradesh, India
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da Silva Lima CH, de Araujo Vanelis Soares JC, de Sousa Ribeiro JL, Muri EMF, de Albuquerque S, Dias LRS. Anti-Trypanosoma cruzi Activity and Molecular Docking Studies of 1Hpyrazolo[ 3, 4-b]pyridine Derivatives. LETT DRUG DES DISCOV 2020. [DOI: 10.2174/1570180816666190305141733] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Untargeted studies led to the development of some pyrazolopyridine
derivatives for the antiparasitic profile, particularly the derivatives containing the structural
carbohydrazide subunit. In this work, we proceeded in the biological screening of 27 N’- (substitutedphenylmethylene)-
4-carbohydrazide-3-methyl-1-phenyl-1H-pyrazolo[3, 4-b]pyridine derivatives against
T. cruzi as well as the cytotoxic evaluation. To obtain more information about the trypanocidal
activity of this class of compounds, we carried out molecular docking simulations to get an insight
into putative targets in T. cruzi.
Methods:
The assays were evaluated against both trypomastigote and amastigote forms of T. cruzi
and cytotoxicity assays on LLCMK2 cells. The predominant conformational compounds were
analyzed and molecular docking simulations performed.
Results:
The results from trypanocidal activity screening of this series showed that just the
compounds with phenyl group at C-6 position exhibited activity and the N’-4-hydroxyphenylmethylene
derivative presented the best profile against both trypomastigote and amastigote
forms of T. cruzi. Docking simulation results showed that this compound has a binding affinity with
both CYP51 and cruzain targets of T. cruzi.
Conclusion:
Our results indicate that the hydroxyl substituent at the N’-substituted-phenylmethylene
moiety and the phenyl ring at C-6 of 1H-pyrazolo[3,4-b]pyridine system are relevant for the
trypanocidal activity of this class of compounds. Also, docking simulations showed that activity
presented can be related to more than one target of the parasite.
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Affiliation(s)
- Camilo Henrique da Silva Lima
- Laboratório de Quimica Medicinal, Universidade Federal Fluminense, Faculdade de Farmacia, Niteroi, Rio de Janeiro, Brazil
| | | | - Joana Lucius de Sousa Ribeiro
- Laboratório de Quimica Medicinal, Universidade Federal Fluminense, Faculdade de Farmacia, Niteroi, Rio de Janeiro, Brazil
| | - Estela Maris Freitas Muri
- Laboratório de Quimica Medicinal, Universidade Federal Fluminense, Faculdade de Farmacia, Niteroi, Rio de Janeiro, Brazil
| | - Sérgio de Albuquerque
- Universidade de Sao Paulo, Departamento de Analises Clinicas, Toxicologicas e Bromatologicas, Av. do Cafe s/n, Ribeirao Preto, SP, 14040-903, Brazil
| | - Luiza Rosaria Sousa Dias
- Laboratório de Quimica Medicinal, Universidade Federal Fluminense, Faculdade de Farmacia, Niteroi, Rio de Janeiro, Brazil
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26
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Suma N, Aruldhas D, Hubert Joe I, Balachandran S, Anuf AR, Sasi A, George J. Vibrational spectra, hydrogen bonding analysis and herbicidal activity study of mefenacet: A DFT approach. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127203] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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27
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Acar çevik U, Osmaniye D. 1,2,4-TRİAZOL YAPISI TAŞIYAN BENZOTİYAZOL TÜREVLERİNİN SENTEZİ VE ANTİFUNGAL AKTİVİTELERİ. DÜZCE ÜNIVERSITESI SAĞLIK BILIMLERI ENSTITÜSÜ DERGISI 2020. [DOI: 10.33631/duzcesbed.593379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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28
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Hagar M, Chaieb K, Parveen S, Ahmed H, Alnoman R. N-alkyl 2-pyridone versus O-alkyl 2-pyridol: Ultrasonic synthesis, DFT, docking studies and their antimicrobial evaluation. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.126926] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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29
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Thalla M, Kant K, Dalchand, Rawat R, Banerjee S. Merged experimental guided computational strategy toward tuberculosis treatment mediated by alveolar macrophages mannose receptor. J Biomol Struct Dyn 2019; 38:5195-5203. [PMID: 31779532 DOI: 10.1080/07391102.2019.1697369] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Macrophage mannose receptor (MMR) is a C-type lectin that regulates the phagocytosis and phagocytosis-lysosome (P-L) fusion in tuberculosis. Mannose-capped lipoarabinomannan, a lipoglycan present at the surface of Mycobacterium tuberculosis, is an important factor in phagocyte attachment and internalization that is specific for MMR. Based on this idea, herein we have designed our experiment to understand the better site-specific delivery against tuberculosis. An experimental outcome was used as a basis to revisit the reverse experimental strategy for tuberculosis management. Stearic mannose was prepared from stearic acid incubation with the D-mannose. Interestingly, stearic mannose explained its internalization via stimulating actin-mediated phagocytic pathway of MMR experimentally. Following, an in silico strategy towards hypothetical designing of various mannose-stearyl conjugates (SBKK1-7) against tuberculosis, as binding promoter of MMR (PDB: 1EGI), was carried out using molecular docking and dynamics approaches. Overall, SPKK-5 viz. ortho stearic mannose showed a higher binding affinity with notable H-bonding and hydrophobic interactions. Pharmacokinetic and toxicity examinations illustrated an ideal range of descriptors values for apex screened compounds. Molecular dynamics simulations have confirmed its significant intactness with the MMR. Ultimately, the whole effort led to the identification of promising hit (SBKK-5), which positively correlates with the experimental work and furthermore need to explore its novel drug delivery systems with improved anti-tubercular therapy.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Maharshi Thalla
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER), Guwahati, Assam, India
| | - Kamal Kant
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER), Guwahati, Assam, India
| | - Dalchand
- Regional Centre for Biotechnology, Faridabad, Haryana, India
| | - Ravi Rawat
- Department of Pharmaceutical Sciences and Technology, Birla Institute of Technology, Ranchi, Jharkhand, India
| | - Subham Banerjee
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER), Guwahati, Assam, India
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30
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Sambandam C, Dhanavel S, Haridoss M, Mannuthusamy G. Docking, Synthesis, Spectral Characterization, and Evaluation of
In Vitro
Antifungal Activity of Bis/Monophenyl‐1‐aryl‐1
H
‐tetrazole‐5‐carboxylate. J Heterocycl Chem 2019. [DOI: 10.1002/jhet.3656] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
| | - Sivakumar Dhanavel
- Department of ChemistryAnnamalai University Annamalai Nagar Chidambaram India
| | - Manikandan Haridoss
- Department of ChemistryAnnamalai University Annamalai Nagar Chidambaram India
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31
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Rana R, Sharma R, Kumar A. Repurposing of Fluvastatin Against Candida albicans CYP450 Lanosterol 14 α-demethylase, a Target Enzyme for Antifungal Therapy: An In silico and In vitro Study. Curr Mol Med 2019; 19:506-524. [PMID: 31109273 DOI: 10.2174/1566524019666190520094644] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 04/24/2019] [Accepted: 05/11/2019] [Indexed: 11/22/2022]
Abstract
Background:
The incidence of fungal infections has increased significantly.
Specifically the cases of candida albicans infection are increasing day by day and their
resistance to clinically approved drugs is a major concern for humans. Various classes
of antifungal drugs are available in the market for the treatment of these infections but
unfortunately, none of them is able to treat the infection.
Objective:
Thus, in the present investigation, we have repurposed the well-known drug
(Fluvastatin) in the treatment of Candida albicans infections by using in silico, in vitro
and ex vivo techniques.
Results:
Firstly, we developed and validated a simple model of CYP45014α-lanosterol
demethylase of Candida albicans by using crystal structure of Mycobacterium
tuberculosis (1EA1). Further, fluvastatin was docked with a validated model of
CYP45014α-lanosterol demethylase and revealed good binding affinity as that of
fluconazole. In vitro results (Percentage growth retardation, Fungal growth kinetics,
Biofilm test and Post antifungal test) have shown good antifungal activity of fluvastatin.
Finally, the results of MTT assay have shown non-cytotoxic effect of fluvastatin in murine
splenocytes and thymocytes.
Results:
Firstly, we developed and validated a simple model of CYP45014α-lanosterol
demethylase of Candida albicans by using crystal structure of Mycobacterium
tuberculosis (1EA1). Further, fluvastatin was docked with a validated model of
CYP45014α-lanosterol demethylase and revealed good binding affinity as that of
fluconazole. In vitro results (Percentage growth retardation, Fungal growth kinetics,
Biofilm test and Post antifungal test) have shown good antifungal activity of fluvastatin.
Finally, the results of MTT assay have shown non-cytotoxic effect of fluvastatin in murine
splenocytes and thymocytes.
Conclusion:
However, further in vivo studies are required to confirm the complete role
of fluvastatin as an antifungal agent.
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Affiliation(s)
- Ritika Rana
- Department of Pharmacology, Indo-Soviet Friendship Pharmacy College (ISFCP), Moga, Punjab, India
| | - Ruchika Sharma
- Department of Biotechnology, Indo-Soviet Friendship College of Professional Studies (ISFCPS), Moga, Punjab, India
| | - Anoop Kumar
- Department of Pharmacology, Indo-Soviet Friendship Pharmacy College (ISFCP), Moga, Punjab, India
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32
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Honorato Siqueira T, Martínez L. Molecular simulations of fluconazole-mediated inhibition of sterol biosynthesis. J Biomol Struct Dyn 2019; 38:1659-1669. [DOI: 10.1080/07391102.2019.1614998] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Tayane Honorato Siqueira
- Institute of Chemistry and Center for Computing in Engineering & Sciences, University of Campinas, Campinas, Brazil
| | - Leandro Martínez
- Institute of Chemistry and Center for Computing in Engineering & Sciences, University of Campinas, Campinas, Brazil
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33
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Sheeja Mol GP, Aruldhas D, Hubert Joe I, Balachandran S, Ronaldo Anuf A, George J, Nadh AG. Structural activity, fungicidal activity and molecular dynamics simulation of certain triphenyl methyl imidazole derivatives by experimental and computational spectroscopic techniques. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 212:105-120. [PMID: 30616164 DOI: 10.1016/j.saa.2018.12.047] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 12/21/2018] [Accepted: 12/26/2018] [Indexed: 06/09/2023]
Abstract
The main objective of the study is to analyze the structural behaviour and fungicidal activity of clotrimazole by experimental and theoretical spectroscopic techniques. Its computational results are correlated with three triphenyl imidazole derivative compounds. The clotrimazole-water complexes formed by hydrogen bonding interactions are investigated at the B3LYP/6-311G(d,p) level. The distributions of the vibrational bands are carried out with the help of normal coordinate analysis (NCA). Hirshfeld surface analysis of clotrimazole is done and the obtained finger print plots reveal the interactions within the compound. The stability of the compounds in water has been investigated by using molecular dynamics simulation (MDS). Molecular docking is done on the compounds in comparison with the native ligand (Lanosterol 14α-demethylase) and standard drug (fluconazole) to study the hydrogen bond energy interaction. The antifungal activity of clotrimazole is analyzed by using two fungal pathogens.
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Affiliation(s)
- G P Sheeja Mol
- Manonmaniam Sundaranar University, Abishekapatti, Tirunelveli 627 012, Tamil Nadu, India; Department of Physics & Research Centre, Nesamony Memorial Christian College, Marthandam 629165, Tamil Nadu, India
| | - D Aruldhas
- Department of Physics & Research Centre, Nesamony Memorial Christian College, Marthandam 629165, Tamil Nadu, India.
| | - I Hubert Joe
- Centre for Molecular and Biophysics Research, Department of Physics, Mar Ivanios College, Thiruvananthapuram 695015, Kerala, India
| | | | - A Ronaldo Anuf
- Department of Biotechnology, Kamaraj College of Engineering and Technology, Virudhunagar 626001, Tamilnadu, India
| | - Jesby George
- Department of Physics, Bishop Moore College, Mavelikara, Alappuzha, Kerala 690110, India
| | - Anuroopa G Nadh
- Department of Computational Biology & Bioinformatics, University of Kerala, Kariavattom, Kerala 695581, India
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34
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Chaudhary M, Kumar N, Baldi A, Chandra R, Arockia Babu M, Madan J. Chloro and bromo-pyrazole curcumin Knoevenagel condensates augmented anticancer activity against human cervical cancer cells: design, synthesis, in silico docking and in vitro cytotoxicity analysis. J Biomol Struct Dyn 2019; 38:200-218. [DOI: 10.1080/07391102.2019.1578264] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Monika Chaudhary
- I. K. Gujral Punjab Technical University, Jalandhar, India
- Department of Medicinal Chemistry, Hindu College of Pharmacy, Sonepat, India
| | - Neeraj Kumar
- Department of Chemistry, University of Delhi, Delhi, India
| | - Ashish Baldi
- Department of Pharmaceutical Sciences and Technology, Maharaja Ranjit Singh Punjab Technical University, Bathinda, India
| | - Ramesh Chandra
- Department of Chemistry, University of Delhi, Delhi, India
- Dr. B.R. Ambedkar Centre for Biomedical Research, University of Delhi, Delhi, India
| | - M. Arockia Babu
- Department of Pharmaceutics, Chandigarh College of Pharmacy, Mohali, India
| | - Jitender Madan
- Department of Pharmaceutics, Chandigarh College of Pharmacy, Mohali, India
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35
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A merged molecular docking, ADME-T and dynamics approaches towards the genus of Arisaema as herpes simplex virus type 1 and type 2 inhibitors. Comput Biol Chem 2019. [DOI: 10.1016/j.compbiolchem.2018.12.005 pmid: 30579134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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36
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Altındağ FD, Sağlık BN, Acar Çevik U, Işıkdağ İ, Özkay Y, Karaca Gençer H. Novel imidazole derivatives as antifungal agents: Synthesis, biological evaluation, ADME prediction and molecular docking studies. PHOSPHORUS SULFUR 2019. [DOI: 10.1080/10426507.2019.1565761] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Firuze Diyar Altındağ
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, Eskişehir, Turkey
| | - Begüm Nurpelin Sağlık
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, Eskişehir, Turkey
- Doping and Narcotic Compounds Analysis Laboratory, Faculty of Pharmacy, Anadolu University, Eskişehir, Turkey
| | - Ulviye Acar Çevik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, Eskişehir, Turkey
- Doping and Narcotic Compounds Analysis Laboratory, Faculty of Pharmacy, Anadolu University, Eskişehir, Turkey
| | - İlhan Işıkdağ
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, Eskişehir, Turkey
| | - Yusuf Özkay
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, Eskişehir, Turkey
- Doping and Narcotic Compounds Analysis Laboratory, Faculty of Pharmacy, Anadolu University, Eskişehir, Turkey
| | - Hülya Karaca Gençer
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Anadolu University, Eskişehir, Turkey
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37
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Kant K, Lal UR, Kumar A, Ghosh M. A merged molecular docking, ADME-T and dynamics approaches towards the genus of Arisaema as herpes simplex virus type 1 and type 2 inhibitors. Comput Biol Chem 2018; 78:217-226. [PMID: 30579134 DOI: 10.1016/j.compbiolchem.2018.12.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 12/10/2018] [Accepted: 12/11/2018] [Indexed: 01/01/2023]
Abstract
An attempt toward screening of phytoconstituents (Arisaema genus) against herpes viruses (HSV-1 and HSV-2) was carried out using in silico approaches. Human HSV-1 and HSV-2 are accountable for cold sores genital herpes, respectively. Two drug targets, namely thymidine kinase (TK; PDB: 2ki5) serine protease (PDB: 1at3) were selected for HSV-1 and HSV-2. Initially, molecular docking tool was employed to screened apex hits phytoconstituents against herpes infections. ADME-T studies of top ranked were also further highlighted to achieve their effectiveness. Following, molecular dynamics studies were also examined to further optimize the stability of ligands. Glide scores and binding interactions of phytoconstituents were compared with Acyclovir, the main drug used in treatment of HSV, the screened top hits exhibited more glide scores and better binding for both HSV-1 and HSV-2 receptors. Additionally, ADME-T showed an ideal range for top hits while molecular dynamics results also illustrated stability of models. Ultimately, the whole efforts reveal to top three most promising hits for HSV-1 (39, 21, 19) and HSV-2 (20, 51, 19) receptors which can be explored further in wet lab experiments as promising agents against HSV infections.
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Affiliation(s)
- Kamal Kant
- Department of Pharmaceutical Sciences and Technology, Birla Institute of Technology, Mesra, Ranchi 835215, Jharkhand, India
| | - Uma Ranjan Lal
- School of Pharmaceutical Sciences, Shoolini University, Post Box 9, Solan 173212, Himachal Pradesh, India
| | - Anoop Kumar
- Department of Pharmacology, Indo-Soviet Friendship College of Pharmacy (ISFCP), Ghal Kalan, Moga 142001, Punjab, India.
| | - Manik Ghosh
- Department of Pharmaceutical Sciences and Technology, Birla Institute of Technology, Mesra, Ranchi 835215, Jharkhand, India.
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38
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Özdemir A, Sever B, Altıntop MD. New Benzodioxole-based Pyrazoline Derivatives: Synthesis and Anticandidal, In silico ADME, Molecular Docking Studies. LETT DRUG DES DISCOV 2018. [DOI: 10.2174/1570180815666180326152726] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Background:
Azoles are commonly used in the treatment and prevention of fungal
infections. They suppress fungal growth by acting on the heme group of lanosterol 14α-demethylase
enzyme (CYP51), thus blocking the biosynthesis of ergosterol.
</P><P>
Objectives: Due to the importance of pyrazolines in the field of antifungal drug design, we aimed to
design and synthesize new pyrazoline-based anticandidal agents.
Methods:
New pyrazoline derivatives were synthesized via the reaction of 1-(chloroacetyl)-3-(2-
thienyl)-5-(1,3-benzodioxol-5-yl)-2-pyrazoline with aryl thiols. These compounds were evaluated
for their in vitro antifungal effects on Candida species. Docking studies were performed to predict
the affinity of the most effective anticandidal agents to substrate binding site of CYP51. Furthermore,
MTT assay was performed to determine the cytotoxic effects of the compounds on NIH/3T3
mouse embryonic fibroblast cell line. A computational study for the prediction of ADME properties
of all compounds was also carried out.
Results:
Compounds 5, 8, 10 and 12 were found as the most potent anticandidal agents against
Candida albicans and Candida glabrata in this series with the same MIC values of ketoconazole
and they also exhibited low toxicity against NIH/3T3 cells. Docking results indicated that all these
compounds showed good binding affinity into the active site of CYP51. In particular, chloro
substituted compounds 8 and 12 bind to CYP51 through direct coordination with the heme group.
According to in silico studies, compound 8 only violated one parameter of Lipinski’s rule of five,
making it a potential orally bioavailable agent.
Conclusion:
Compound 8 was defined as a promising candidate for further in vitro and in vivo
studies.
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Affiliation(s)
- Ahmet Özdemir
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, 26470 Eskişehir, Turkey
| | - Belgin Sever
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, 26470 Eskişehir, Turkey
| | - Mehlika Dilek Altıntop
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, 26470 Eskişehir, Turkey
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39
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Arandkar V, Vaarla K, Vedula RR. Facile one pot multicomponent synthesis of novel 4-(benzofuran-2-yl)-2-(3-(aryl/heteryl)-5-(aryl/heteryl)-4,5-dihydro-1 H-pyrazol-1yl)thiazole derivatives. SYNTHETIC COMMUN 2018. [DOI: 10.1080/00397911.2018.1440600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
- Varun Arandkar
- Department of Chemistry, National Institute of Technology, Warangal, Telangana, India
| | - Krishnaiah Vaarla
- Department of Chemistry, National Institute of Technology, Warangal, Telangana, India
| | - Rajeswar Rao Vedula
- Department of Chemistry, National Institute of Technology, Warangal, Telangana, India
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40
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Shukla R, Shukla H, Sonkar A, Pandey T, Tripathi T. Structure-based screening and molecular dynamics simulations offer novel natural compounds as potential inhibitors of Mycobacterium tuberculosis isocitrate lyase. J Biomol Struct Dyn 2017; 36:2045-2057. [DOI: 10.1080/07391102.2017.1341337] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Rohit Shukla
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Harish Shukla
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Amit Sonkar
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Tripti Pandey
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Timir Tripathi
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
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41
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Synthesis, Molecular Docking Studies, and Antifungal Activity Evaluation of New Benzimidazole-Triazoles as Potential Lanosterol 14α-Demethylase Inhibitors. J CHEM-NY 2017. [DOI: 10.1155/2017/9387102] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Due to anticandidal importance of azole compounds, a new series of benzimidazole-triazole derivatives(5a–5s)were designed and synthesized as ergosterol inhibitors. The chemical structures of the target compounds were characterized by spectroscopic methods. The final compounds were screened for antifungal activity againstCandida glabrata(ATCC 90030),Candida krusei(ATCC 6258),Candida parapsilosis(ATCC 22019), andCandida albicans(ATCC 24433). Compounds5iand5sexhibited significant inhibitory activity againstCandidastrains with MIC50values ranging from 0.78 to 1.56 μg/mL. Cytotoxicity results revealed that IC50values of compounds5iand5sagainst NIH/3T3 are significantly higher than their MIC50values. Effect of the compounds5iand5sagainst ergosterol biosynthesis was determined by LC-MS-MS analysis. Both compounds caused a significant decrease in the ergosterol level. The molecular docking studies were performed to investigate the interaction modes between the compounds and active site of lanosterol 14-α-demethylase (CYP51), which is as a target enzyme for anticandidal azoles. Theoretical ADME predictions were also calculated for final compounds.
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