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Shi J, Zhao LX, Wang JY, Ye T, Wang M, Gao S, Ye F, Fu Y. The novel 4-hydroxyphenylpyruvate dioxygenase inhibitors in vivo and in silico approach: 3D-QSAR analysis, molecular docking, bioassay and molecular dynamics. ARAB J CHEM 2022. [DOI: 10.1016/j.arabjc.2022.103919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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Patrício RPS, Videira PA, Pereira F. A computer-aided drug design approach to discover tumour suppressor p53 protein activators for colorectal cancer therapy. Bioorg Med Chem 2022; 53:116530. [PMID: 34861473 DOI: 10.1016/j.bmc.2021.116530] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 11/02/2021] [Accepted: 11/19/2021] [Indexed: 02/03/2023]
Abstract
Colorectal cancer (CRC) is the third most detected cancer and the second foremost cause of cancer deaths in the world. Intervention targeting p53 provides potential therapeutic strategies, but thus far no p53-based therapy has been successfully translated into clinical cancer treatment. Here we developed a Quantitative Structure-Activity Relationships (QSAR) classification models using empirical molecular descriptors and fingerprints to predict the activity against the p53 protein, using the potency value with the active or inactive label, were developed. These models were built using in total 10,505 molecules that were extracted from the ChEMBL, ZINC and Reaxys® databases, and recent literature. Three machine learning (ML) techniques e.g., Random Forest, Support Vector Machine, Convolutional Neural Network were explored to build models for p53 inhibitor prediction. The performances of the models were successfully evaluated by internal and external validation. Moreover, based on the best in silico p53 model, a virtual screening campaign was carried out using 1443 FDA-approved drugs that were extracted from the ZINC database. A list of virtual screening hits was assented on base of some limits established in this approach, such as: (1) probability of being active against p53; (2) applicability domain; (3) prediction of the affinity between the p53, and ligands, through molecular docking. The most promising according to the limits established above was dihydroergocristine. This compound revealed cytotoxic activity against a p53-expressing CRC cell line with an IC50 of 56.8 µM. This study demonstrated that the computer-aided drug design approach can be used to identify previously unknown molecules for targeting p53 protein with anti-cancer activity and thus pave the way for the study of a therapeutic solution for CRC.
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Affiliation(s)
- Rui P S Patrício
- LAQV and REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal; UCIBIO, Departamento Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Paula A Videira
- UCIBIO, Departamento Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Florbela Pereira
- LAQV and REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal.
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Panigrahi D, Mishra A, Sahu SK. Rational in silico drug design of HIV-RT inhibitors through G-QSAR and molecular docking study of 4-arylthio and 4-aryloxy-3-iodopyridine-2(1-H)-one derivative. BENI-SUEF UNIVERSITY JOURNAL OF BASIC AND APPLIED SCIENCES 2020. [DOI: 10.1186/s43088-020-00075-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Human immunodeficiency virus infection and acquired immune deficiency syndrome (HIV/AIDS) is a spectrum of conditions caused by infection with the human immunodeficiency virus (HIV). Antiretroviral therapy (ART) against HIV infection offers the promise of controlling disease progression and prolonging the survival of HIV-infected patients. Reverse transcriptase (RT) inhibitors remain the cornerstone of the drug regimen to treat AIDS. In this direction, by using group-based QSAR study (G-QSAR), identification of the structural need for the development of lead structure with reverse transcriptase inhibition on 97 reported structures was carried out. Docking analysis was performed further and suggested the structural properties required for binding affinity with the receptor. The molecules in the data set were fragmented into six (R1, R2, R3, R4, R5, and R6) by applying the fragmentation pattern. Three G-QSAR models were selected based on the statistical significance of the model. The molecular docking study was performed to explain the structural properties required for the design of potent HIV-RT inhibitors.
Results
The statistically validated QSAR models reveal the presence of higher hydrophobic groups containing single-bonded –Br atom, 2 aromatic bonded –NH group with less electronegativity, and entropic interaction fields at R2 essential for better anti-HIV activity. The presence of a lipophilic group at R3, oxygen and sulfur connected with two aromatic bonds at R4, and –CH3 group at R5 was fruitful for reverse transcriptase inhibition. Docking studies of the selected inhibitors with the active site of reverse transcriptase enzyme showed hydrogen bond, Van der Waal’s, charge, aromatic, and π–π interactions with residues present at the active site.
Conclusion
The results of the generated models provide significant site-specific insight into the structural requirements for reverse transcriptase inhibition during the design and development of novel anti-HIV compounds. Molecular docking study revealed the binding interaction between the ligand and the receptor which gave insight towards the structure-based design for the discovery of more potent compounds with better activity against HIV infection.
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Pharmacophore modelling, QSAR study, molecular docking and insilico ADME prediction of 1,2,3-triazole and pyrazolopyridones as DprE1 inhibitor antitubercular agents. SN APPLIED SCIENCES 2020. [DOI: 10.1007/s42452-020-2638-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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Singh A, Somvanshi P, Grover A. Pyrazinamide drug resistance in RpsA mutant (∆438A) of Mycobacterium tuberculosis: Dynamics of essential motions and free-energy landscape analysis. J Cell Biochem 2019; 120:7386-7402. [PMID: 30390330 DOI: 10.1002/jcb.28013] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 10/10/2018] [Indexed: 01/24/2023]
Abstract
Pyrazinamide is an essential first-line antitubercular drug which plays pivotal role in tuberculosis treatment. It is a prodrug that requires amide hydrolysis by mycobacterial pyrazinamidase enzyme for conversion into pyrazinoic acid (POA). POA is known to target ribosomal protein S1 (RpsA), aspartate decarboxylase (PanD), and some other mycobacterial proteins. Spontaneous chromosomal mutations in RpsA have been reported for phenotypic resistance against pyrazinamide. We have constructed and validated 3D models of the native and Δ438A mutant form of RpsA protein. RpsA protein variants were then docked to POA and long range molecular dynamics simulations were carried out. Per residue binding free-energy calculations, free-energy landscape analysis, and essential dynamics analysis were performed to outline the mechanism underlying the high-level PZA resistance conferred by the most frequently occurring deletion mutant of RpsA. Our study revealed the conformational modulation of POA binding site due to the disruptive collective modes of motions and increased conformational flexibility in the mutant than the native form. Residue wise MMPBSA decomposition and protein-drug interaction pattern revealed the difference of energetically favorable binding site in the wild-type (WT) protein in comparison with the mutant. Analysis of size and shape of minimal energy landscape area delineated higher stability of the WT complex than the mutant form. Our study provides mechanistic insights into pyrazinamide resistance in Δ438A RpsA mutant, and the results arising out of this study will pave way for design of novel and effective inhibitors targeting the resistant strains of Mycobacterium tuberculosis.
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Affiliation(s)
- Aditi Singh
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India.,Department of Biotechnology, TERI School of Advanced Studies, Vasant Kunj Institutional Area, New Delhi, India
| | - Pallavi Somvanshi
- Department of Biotechnology, TERI School of Advanced Studies, Vasant Kunj Institutional Area, New Delhi, India
| | - Abhinav Grover
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
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Singh A, Das M, Grover A. Molecular mechanism of acetoacetyl-CoA enhanced kinetics for increased bioplastic production from Cupriavidus necator 428. J Biomol Struct Dyn 2019; 38:827-840. [PMID: 30836854 DOI: 10.1080/07391102.2019.1590239] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Polyhydroxyalkanoates are gaining importance due to their biodegradable nature and close analogy to plastics. Polyhydroxybutyrate (PHB) is the most widely used bioplastic from polyalkanoate family, which is produced by a legion of bacterial species via phbCAB operon encoding β-ketothiolase (PhaA), NADPH-dependent acetoacetyl-coenzyme A (acetoacetyl-CoA) reductase (PhaB) and polyhydroxyalkanoate synthase (PhaC). Augmentation in the activity of these enzymes is promising for increased PHB production which is achieved by enzyme engineering strategies including non-structural and structural approaches. Our study is deployed on directed evolution-based experimentally reported mutants of PhaB enzyme with increased efficiency due to impact on critical structural factors. We have analyzed and compared the native PhaB with two of its variants Q47L and T173S in complex with their cofactor i.e. NADPH as well as the substrate i.e. acetoacetyl-CoA, via long range molecular dynamics simulations. Interaction profile, MMPBSA, essential dynamics, and free energy landscape analysis revealed that the enzyme efficiency is critically affected by cofactor interactions. It was also observed that mutants have higher equilibrium constant with lesser but optimal affinity for substrate and cofactor than the wild type, which might be the reason for increased efficiency of the mutants via enhanced substrate and cofactor exchange rate. Our study provides insights into the cofactor and substrate binding affinities to PhaB enzyme at atomistic level, which will facilitate designing of highly efficient PhaB enzymes for increased PHB production. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Aditi Singh
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India.,Department of Biotechnology, TERI School of Advanced Studies, Vasant Kunj, New Delhi, India
| | - Mriganko Das
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Abhinav Grover
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
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Safarizadeh H, Garkani-Nejad Z. Molecular docking, molecular dynamics simulations and QSAR studies on some of 2-arylethenylquinoline derivatives for inhibition of Alzheimer's amyloid-beta aggregation: Insight into mechanism of interactions and parameters for design of new inhibitors. J Mol Graph Model 2019; 87:129-143. [DOI: 10.1016/j.jmgm.2018.11.019] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 11/18/2018] [Accepted: 11/30/2018] [Indexed: 02/06/2023]
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Safarizadeh H, Garkani-Nejad Z. Investigation of MI-2 analogues as MALT1 inhibitors to treat of diffuse large B-Cell lymphoma through combined molecular dynamics simulation, molecular docking and QSAR techniques and design of new inhibitors. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2018.12.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Tong J, Jiang G, Li L, Li Y. Molecular Virtual Screening Studies of Herbicidal Sulfonylurea Analogues Using Molecular Docking and Topomer CoMFA Research. J STRUCT CHEM+ 2019. [DOI: 10.1134/s0022476619020057] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Singh A, Somvanshi P, Grover A. Drug repurposing against arabinosyl transferase (EmbC) of Mycobacterium tuberculosis: Essential dynamics and free energy minima based binding mechanics analysis. Gene 2019; 693:114-126. [PMID: 30716439 DOI: 10.1016/j.gene.2019.01.029] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 12/20/2018] [Accepted: 01/02/2019] [Indexed: 01/10/2023]
Abstract
Arabinosyl tranferases (embA, embB, embC) are the key enzymes responsible for biogenesis of arabinan domain of arabinogalactan (AG) and lipoarabinomannan (LAM), two major heteropolysaccharide constituents of the peculiar mycobacterial cell envelope. EmbC is predominantly responsible for LAM synthesis and has been commonly associated with Ethambutol resistance. We have screened the FDA library against EmbC to reposition a drug better than Ethambutol with higher binding affinity to Embc. High throughput virtual screening followed by extra precision docking using Glide gave two best leads i.e. Terlipressin and Amikacin with docking score of -11.39 kcal/mol and -10.71 kcal/mol, respectively. Binding mechanics of the selected drugs was elucidated through long range molecular dynamics simulations (100 ns) using binding free energy rescoring, essential dynamics and free energy minima based approaches, thus revealing the most stable binding modes of Terlipressin with EmbC. Our study establishes the EmbC binding potential of the repurposed drugs Terlipressin and Amikacin.
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Affiliation(s)
- Aditi Singh
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India; Department of Biotechnology, TERI School of Advanced Studies, Plot No. 10, Vasant Kunj Institutional Area, Vasant Kunj, New Delhi, 110070, India
| | - Pallavi Somvanshi
- Department of Biotechnology, TERI School of Advanced Studies, Plot No. 10, Vasant Kunj Institutional Area, Vasant Kunj, New Delhi, 110070, India.
| | - Abhinav Grover
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India.
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Kumar A, Alam A, Grover S, Pandey S, Tripathi D, Kumari M, Rani M, Singh A, Akhter Y, Ehtesham NZ, Hasnain SE. Peptidyl-prolyl isomerase-B is involved in Mycobacterium tuberculosis biofilm formation and a generic target for drug repurposing-based intervention. NPJ Biofilms Microbiomes 2019; 5:3. [PMID: 30675370 PMCID: PMC6333787 DOI: 10.1038/s41522-018-0075-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 10/15/2018] [Indexed: 01/03/2023] Open
Abstract
Tuberculosis (TB), a disease caused by Mycobacterium tuberculosis (M.tb), takes one human life every 15 s globally. Disease relapse occurs due to incomplete clearance of the pathogen and reactivation of the antibiotic tolerant bacilli. M.tb, like other bacterial pathogens, creates an ecosystem of biofilm formed by several proteins including the cyclophilins. We show that the M.tb cyclophilin peptidyl-prolyl isomerase (PpiB), an essential gene, is involved in biofilm formation and tolerance to anti-mycobacterial drugs. We predicted interaction between PpiB and US FDA approved drugs (cyclosporine-A and acarbose) by in-silico docking studies and this was confirmed by surface plasmon resonance (SPR) spectroscopy. While all these drugs inhibited growth of Mycobacterium smegmatis (M.smegmatis) when cultured in vitro, acarbose and cyclosporine-A showed bacteriostatic effect while gallium nanoparticle (GaNP) exhibited bactericidal effect. Cyclosporine-A and GaNP additionally disrupted M.tb H37Rv biofilm formation. Co-culturing M.tb in their presence resulted in significant (2–4 fold) decrease in dosage of anti-tubercular drugs- isoniazid and ethambutol. Comparison of the cyclosporine-A and acarbose binding sites in PpiB homologues of other biofilm forming infectious pathogens revealed that these have largely remained unaltered across bacterial species. Targeting bacterial biofilms could be a generic strategy for intervention against bacterial pathogens. Tuberculosis, caused by Mycobacterium tuberculosis, is the leading cause of death due to a single infectious agent. New therapeutic options are needed, and repurposing clinically approved drugs to destroy biofilms is an attractive approach, as these microbial communities are often less susceptible to antibiotics. A team lead by Seyed Hasnain at the Indian Institute of Technology Delhi identified an enzyme, PpiB, from M. tuberculosis that promoted biofilm formation and showed that PpiB interacts with several drugs that are currently used to treat diabetes, immunological diseases and cancer. These drugs destabilise M. tuberculosis biofilms in culture and enhanced the potency of two current anti-tuberculosis antibiotics. Future work is needed to test these medications against tuberculosis in humans, but given PpiB is found in different bacteria, there may be broader promise of using these repurposed drugs to combat other infections.
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Affiliation(s)
- Ashutosh Kumar
- 1JH-Institute of Molecular Medicine, Jamia Hamdard, New Delhi, India.,Present Address: Department of Microbiology, Tripura Central University, Suryamaninagar, Agartala, Tripura India
| | - Anwar Alam
- 1JH-Institute of Molecular Medicine, Jamia Hamdard, New Delhi, India.,2Molecular Infection and Functional Biology Lab, Kusuma School of Biological Sciences, Indian Institute of Technology-Delhi, New Delhi, India
| | - Sonam Grover
- 1JH-Institute of Molecular Medicine, Jamia Hamdard, New Delhi, India
| | - Saurabh Pandey
- 3National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, India.,11Present Address: Department of Biochemistry, Jamia Hamdard, New Delhi, India
| | - Deeksha Tripathi
- 2Molecular Infection and Functional Biology Lab, Kusuma School of Biological Sciences, Indian Institute of Technology-Delhi, New Delhi, India.,4Department of Microbiology, Central University of Rajasthan, Ajmer, Rajasthan India
| | - Monika Kumari
- 5Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, Himachal Pradesh, India
| | - Mamta Rani
- 6Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology-Delhi, New Delhi, India
| | - Aditi Singh
- 7School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Yusuf Akhter
- 8Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Lucknow, India
| | - Nasreen Z Ehtesham
- 3National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, India
| | - Seyed E Hasnain
- 1JH-Institute of Molecular Medicine, Jamia Hamdard, New Delhi, India.,2Molecular Infection and Functional Biology Lab, Kusuma School of Biological Sciences, Indian Institute of Technology-Delhi, New Delhi, India.,9Dr Reddy's Institute of Life Sciences, University of Hyderabad Campus, Prof CR Rao Road, Hyderabad, India
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Tong J, Jiang G, Li L, Li Y. Molecular Docking and 3D QSAR Research of Indolocarbazole Series as Cyclin-Dependent Kinase Inhibitors. J STRUCT CHEM+ 2018. [DOI: 10.1134/s0022476618070065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Kumar N, Singh A, Grover S, Kumari A, Kumar Dhar P, Chandra R, Grover A. HHV-5 epitope: A potential vaccine candidate with high antigenicity and large coverage. J Biomol Struct Dyn 2018; 37:2098-2109. [PMID: 30044169 DOI: 10.1080/07391102.2018.1477620] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Outbreak of Human Herpes virus-5 (HHV-5) infection in emerging countries has raised worldwide health concern owing to prevalence of congenital impairments and life threatening consequences in immunocompromised individuals. Thus, there lies an impending need to develop vaccine against HHV-5. HHV-5 enters into host cells with the help of necessary components glycoprotein B (gB) and H/L. In this study, the conformational linear B-cell and T-cell epitopes for gB of HHV-5 have been predicted using conformational approaches, for their possible collective use as vaccine candidates. We examined epitope's interactions with major histocompatibility complexes using molecular docking and also investigated their stable binding with specific toll like receptor-2 (TLR2), present on host cells during HHV-5 infection. Predicted MHC-I epitope 'LVAIAVVII' with high antigenicity and large coverage of HLA alleles was found to superimpose on MHC-II epitope (Rank 1) and was also identified to be the core sequence of putative B cell epitope 'ILVAIAVVIITYLI'. Resulting epitope was found to have consistent interaction with TLR2 during long term (100 ns) MD run. We also validated this nonamer epitope for its dissimilarity with human genome and high population coverage, suggesting it to be a potential vaccine candidate with higher coverage for both the MHC alleles of Indian population. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Neeraj Kumar
- a Drug Discovery and Development Laboratory, Department of Chemistry , University of Delhi , New Delhi , India
| | - Aditi Singh
- b Department of Biotechnology , TERI School of Advanced Studies , New Delhi , India.,c School of Biotechnology , Jawaharlal Nehru University , New Delhi , India
| | - Sonam Grover
- d Kusuma School of Biological Sciences , IIT Delhi , New Delhi , India
| | - Anchala Kumari
- b Department of Biotechnology , TERI School of Advanced Studies , New Delhi , India.,c School of Biotechnology , Jawaharlal Nehru University , New Delhi , India
| | - Pawan Kumar Dhar
- c School of Biotechnology , Jawaharlal Nehru University , New Delhi , India
| | - Ramesh Chandra
- a Drug Discovery and Development Laboratory, Department of Chemistry , University of Delhi , New Delhi , India
| | - Abhinav Grover
- c School of Biotechnology , Jawaharlal Nehru University , New Delhi , India
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Tong J, Lei S, Qin S, Wang Y. QSAR studies of TIBO derivatives as HIV-1 reverse transcriptase inhibitors using HQSAR, CoMFA and CoMSIA. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.05.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Singh A, Singh A, Grover S, Pandey B, Kumari A, Grover A. Wild-type catalase peroxidase vs G279D mutant type: Molecular basis of Isoniazid drug resistance in Mycobacterium tuberculosis. Gene 2018; 641:226-234. [DOI: 10.1016/j.gene.2017.10.047] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 10/16/2017] [Indexed: 11/29/2022]
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Aggarwal M, Singh A, Grover S, Pandey B, Kumari A, Grover A. Role of pncA gene mutations W68R and W68G in pyrazinamide resistance. J Cell Biochem 2017; 119:2567-2578. [PMID: 28980723 DOI: 10.1002/jcb.26420] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 10/03/2017] [Indexed: 12/12/2022]
Abstract
Mycobacterium tuberculosis (Mtb) resistance toward anti-tuberculosis drugs is a widespread problem. Pyrazinamide (PZA) is a first line antitubercular drug that kills semi-dormant bacilli when converted into its activated form, that is, pyrazinoic acid (POA) by Pyrazinamidase (PZase) enzyme coded by pncA gene. In this study, we conducted several analyses on native and mutant structures (W68R, W68G) of PZase before and after docking with the PZA drug to explore the molecular mechanism behind PZA resistance caused due to pncA mutations. Structural changes caused by mutations were studied with respect to their effects on functionality of protein. Docking was performed to analyze the protein-drug binding and comparative analysis was done to observe how the mutations affect drug binding affinity and binding site on protein. Native PZase protein was observed to have the maximum binding affinity in terms of docking score as well as shape complementarity in comparison to the mutant forms. Molecular dynamics simulation analyses showed that mutation in the 68th residue of protein results in a structural change at its active site which further affects the biological function of protein, that is, conversion of PZA to POA. Mutations in the protein thereby led to PZA resistance in the bacterium due to the inefficient binding.
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Affiliation(s)
- Mansi Aggarwal
- Ami, ty Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, India
| | - Aditi Singh
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India.,Department of Biotechnology, TERI University, Vasant Kunj, New Delhi, India
| | - Sonam Grover
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
| | - Bharati Pandey
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Anchala Kumari
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India.,Department of Biotechnology, TERI University, Vasant Kunj, New Delhi, India
| | - Abhinav Grover
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
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Interplay of thermochemistry and Structural Chemistry, the journal (volume 27, 2016, issues 3–4) and the discipline. Struct Chem 2017. [DOI: 10.1007/s11224-017-0983-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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19
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Joshi K, Goyal S, Grover S, Jamal S, Singh A, Dhar P, Grover A. Novel group-based QSAR and combinatorial design of CK-1δ inhibitors as neuroprotective agents. BMC Bioinformatics 2016; 17:515. [PMID: 28155653 PMCID: PMC5260052 DOI: 10.1186/s12859-016-1379-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Background Tar DNA binding protein 43 (TDP-43) hyperphosphorylation, caused by Casein kinase 1 (CK-1) protein isoforms, is associated with the onset and progression of Amyotrophic Lateral Sclerosis (ALS). Among the reported isoforms and splice variants of CK-1 protein superfamily, CK-1δ is known to phosphorylate different serine and threonine sites on TDP-43 protein in vitro and thus qualifies as a potential target for ALS treatment. Results The developed GQSAR (group based quantitative structure activity relationship) model displayed satisfactory statistical parameters for the dataset of experimentally reported N-Benzothiazolyl-2-Phenyl Acetamide derivatives. A combinatorial library of molecules was also generated and the activities were predicted using the statistically sound GQSAR model. Compounds with higher predicted inhibitory activity were screened against CK-1δ that resulted in to the potential novel leads for CK-1δ inhibition. Conclusions In this study, a robust fragment based QSAR model was developed on a congeneric set of experimentally reported molecules and using combinatorial library approach, a series of molecules were generated from which we report two top scoring, CK-1δ inhibitors i.e., CHC (6-benzyl-2-cyclopropyl-4-{[(4-cyclopropyl-6-ethyl-1,3-benzothiazol-2-yl)carbamoyl]methyl}j-3-fluorophenyl hydrogen carbonate) and DHC (6-benzyl-4-{[(4-cyclopropyl-6-ethyl-1,3-benzothiazol-2-yl)carbamoyl]methyl}-2-(decahydronaphthalen-1-yl)-3-hydroxyphenyl hydrogen carbonate) with binding energy of −6.11 and −6.01 kcal/mol, respectively.
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Affiliation(s)
- Kopal Joshi
- Amity School of Biotechnology, Amity University, Noida, Uttar Pradesh, 201303, India
| | - Sukriti Goyal
- Department of Bioscience and Biotechnology, Banasthali University, Tonk, Rajasthan, 304022, India
| | - Sonam Grover
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Salma Jamal
- Department of Bioscience and Biotechnology, Banasthali University, Tonk, Rajasthan, 304022, India
| | - Aditi Singh
- Department of Biotechnology, TERI University, New Delhi, 110070, India
| | - Pawan Dhar
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Abhinav Grover
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India.
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