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Raju B, Sapra B, Silakari O. 3D-QSAR assisted identification of selective CYP1B1 inhibitors: an effective bioisosteric replacement/molecular docking/electrostatic complementarity analysis. Mol Divers 2023; 27:2673-2693. [PMID: 36441444 DOI: 10.1007/s11030-022-10574-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/20/2022] [Indexed: 11/29/2022]
Abstract
Cytochrome P450-1B1 is a majorly overexpressed drug-metabolizing enzyme in tumors and is responsible for inactivation and subsequent resistance to a variety of anti-cancer drugs, i.e., docetaxel, tamoxifen, and cisplatin. In the present study, a 3D quantitative structure-activity relationship (3D-QSAR) model has been constructed for the identification, design, and optimization of novel CYP1B1 inhibitors. The model has been built using a set of 148 selective CYP1B1 inhibitors. The developed model was evaluated based on certain statistical parameters including q2 and r2 which showed the acceptable predictive and descriptive capability of the generated model. The developed 3D-QSAR model assisted in understanding the key molecular fields which were firmly related to the selective CYP1B1 inhibition. A theoretic approach for the generation of new lead compounds with optimized CYP1B1 receptor affinity has been performed utilizing bioisosteric replacement analysis. These generated molecules were subjected to a developed 3D-QSAR model to predict the inhibitory activity potentials. Furthermore, these compounds were scrutinized through the activity atlas model, molecular docking, electrostatic complementarity, molecular dynamics, and waterswap analysis. The final hits might act as selective CYP1B1 inhibitors which could address the issue of resistance. This 3D-QSAR includes several chemically diverse selective CYP1B1 receptor ligands and well accounts for the individual ligand's inhibition affinities. These features of the developed 3D-QSAR model will ensure future prospective applications of the model to speed up the identification of new potent and selective CYP1B1 receptor ligands.
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Affiliation(s)
- Baddipadige Raju
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, 147002, India
| | - Bharti Sapra
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, 147002, India
| | - Om Silakari
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, 147002, India.
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2
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Biswas D, Somkuwar BG, Borah JC, Varadwaj PK, Gupta S, Khan ZA, Mondal G, Chattoraj A, Deb L. Phytochemical mediated modulation of COX-3 and NFκB for the management and treatment of arthritis. Sci Rep 2023; 13:13612. [PMID: 37604838 PMCID: PMC10442333 DOI: 10.1038/s41598-023-37729-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 06/27/2023] [Indexed: 08/23/2023] Open
Abstract
In this study, we investigated whether zerumbone (ZBN), ellagic acid (ELA) and quercetin (QCT), the plant-derived components, can modulate the role of COX-3 or cytokines liable in arthritic disorder. Initially, the effect of ZBN, ELA, and QCT on inflammatory process was investigated using in-vitro models. In-silico docking and molecular dynamics study of these molecules with respective targets also corroborate with in-vitro studies. Further, the in-vivo anti-arthritic potential of these molecules in Complete Freund's adjuvant (CFA)-induced arthritic rats was confirmed. CFA increases in TNF-α and IL-1β levels in the arthritic control animals were significantly (***p < 0.001) attenuated in the ZBN- and ELA-treated animals. CFA-induced attenuation in IL-10 levels recovered under treatment. Moreover, ELA attenuated CFA-induced upregulation of COX-3 and ZBN downregulated CFA-triggered NFκB expression in arthritic animals. The bonding patterns of zerumbone in the catalytic sites of targets provide a useful hint in designing and developing suitable derivatives that can be used as a potential drug. To our best knowledge, the first time we are reporting the role of COX-3 in the treatment of arthritic disorders which could provide a novel therapeutic approach for the treatment of inflammatory disorders.
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Affiliation(s)
- Dipak Biswas
- Natural Product Chemistry and Pharmacology Programme, Medicinal Plants and Horticulture Resources Division, Institute of Bioresources and Sustainable Development, (An Autonomous Institute of Department of Biotechnology, Government of India), Takyelpat, Imphal, 795001, Manipur, India
| | - Bharat Gopalrao Somkuwar
- Bioinformatics and Bioresources Database Division, Institute of Bioresources and Sustainable Development, (An Autonomous Institute of Department of Biotechnology, Government of India), Takyelpat, Imphal, 795001, Manipur, India
| | - Jagat Chandra Borah
- Natural Product Chemistry and Pharmacology Programme, Medicinal Plants and Horticulture Resources Division, Institute of Bioresources and Sustainable Development, (An Autonomous Institute of Department of Biotechnology, Government of India), Takyelpat, Imphal, 795001, Manipur, India
- Institute of Advanced Study in Science and Technology, (An Autonomous Institute Under Department of Science & Technology, Govt. of India) Vigyan Path, Paschim Boragaon Garchuk, Guwahati, 781035, Assam, India
| | - Pritish Kumar Varadwaj
- Department of Applied Sciences, Indian Institute of Information Technology, Devghat, Jhalwa, Allahabad, 211015, Uttar Pradesh, India
| | - Saurabh Gupta
- Department of Applied Sciences, Indian Institute of Information Technology, Devghat, Jhalwa, Allahabad, 211015, Uttar Pradesh, India
| | - Zeeshan Ahmad Khan
- Biological Rhythm Laboratory, Animal Resources Programme, Institute of Bioresources and Sustainable Development, (An Autonomous Institute of Department of Biotechnology, Government of India), Takyelpat, Imphal, 795001, Manipur, India
| | - Gopinath Mondal
- Biological Rhythm Laboratory, Animal Resources Programme, Institute of Bioresources and Sustainable Development, (An Autonomous Institute of Department of Biotechnology, Government of India), Takyelpat, Imphal, 795001, Manipur, India
| | - Asamanja Chattoraj
- Biological Rhythm Laboratory, Animal Resources Programme, Institute of Bioresources and Sustainable Development, (An Autonomous Institute of Department of Biotechnology, Government of India), Takyelpat, Imphal, 795001, Manipur, India
- Department of Animal Science, Kazi Nazrul University, Paschim Bardhaman, Asansol, 71330, West Bengal, India
| | - Lokesh Deb
- Natural Product Chemistry and Pharmacology Programme, Medicinal Plants and Horticulture Resources Division, Institute of Bioresources and Sustainable Development, (An Autonomous Institute of Department of Biotechnology, Government of India), Takyelpat, Imphal, 795001, Manipur, India.
- Institute of Bioresources and Sustainable Development-Regional Centre, Sikkim (Department of Biotechnology, Government of India), 5th Mile, Near Metro Point, Tadong, Gangtok, 737102, Sikkim, India.
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3
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Yang Z, Liu J, Zhu X, Yang F, Zhang Q, Shah HA. FragDPI: a novel drug-protein interaction prediction model based on fragment understanding and unified coding. FRONTIERS OF COMPUTER SCIENCE 2022; 17:175903. [PMID: 36532946 PMCID: PMC9745276 DOI: 10.1007/s11704-022-2163-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 07/11/2022] [Indexed: 06/17/2023]
Abstract
UNLABELLED Prediction of drug-protein binding is critical for virtual drug screening. Many deep learning methods have been proposed to predict the drug-protein binding based on protein sequences and drug representation sequences. However, most existing methods extract features from protein and drug sequences separately. As a result, they can not learn the features characterizing the drug-protein interactions. In addition, the existing methods encode the protein (drug) sequence usually based on the assumption that each amino acid (atom) has the same contribution to the binding, ignoring different impacts of different amino acids (atoms) on the binding. However, the event of drug-protein binding usually occurs between conserved residue fragments in the protein sequence and atom fragments of the drug molecule. Therefore, a more comprehensive encoding strategy is required to extract information from the conserved fragments. In this paper, we propose a novel model, named FragDPI, to predict the drug-protein binding affinity. Unlike other methods, we encode the sequences based on the conserved fragments and encode the protein and drug into a unified vector. Moreover, we adopt a novel two-step training strategy to train FragDPI. The pre-training step is to learn the interactions between different fragments using unsupervised learning. The fine-tuning step is for predicting the binding affinities using supervised learning. The experiment results have illustrated the superiority of FragDPI. ELECTRONIC SUPPLEMENTARY MATERIAL Supplementary material is available for this article at 10.1007/s11704-022-2163-9 and is accessible for authorized users.
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Affiliation(s)
- Zhihui Yang
- Institute of Artificial Intelligence, School of Computer Science, Wuhan University, Wuhan, 430072 China
| | - Juan Liu
- Institute of Artificial Intelligence, School of Computer Science, Wuhan University, Wuhan, 430072 China
| | - Xuekai Zhu
- Institute of Artificial Intelligence, School of Computer Science, Wuhan University, Wuhan, 430072 China
| | - Feng Yang
- Institute of Artificial Intelligence, School of Computer Science, Wuhan University, Wuhan, 430072 China
| | - Qiang Zhang
- Institute of Artificial Intelligence, School of Computer Science, Wuhan University, Wuhan, 430072 China
| | - Hayat Ali Shah
- Institute of Artificial Intelligence, School of Computer Science, Wuhan University, Wuhan, 430072 China
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Raju B, Narendra G, Verma H, Kumar M, Sapra B, Kaur G, jain SK, Silakari O. Machine Learning Enabled Structure-Based Drug Repurposing Approach to Identify Potential CYP1B1 Inhibitors. ACS OMEGA 2022; 7:31999-32013. [PMID: 36120033 PMCID: PMC9476183 DOI: 10.1021/acsomega.2c02983] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
Drug-metabolizing enzyme (DME)-mediated pharmacokinetic resistance of some clinically approved anticancer agents is one of the main reasons for cancer treatment failure. In particular, some commonly used anticancer medicines, including docetaxel, tamoxifen, imatinib, cisplatin, and paclitaxel, are inactivated by CYP1B1. Currently, no approved drugs are available to treat this CYP1B1-mediated inactivation, making the pharmaceutical industries strive to discover new anticancer agents. Because of the extreme complexity and high risk in drug discovery and development, it is worthwhile to come up with a drug repurposing strategy that may solve the resistance problem of existing chemotherapeutics. Therefore, in the current study, a drug repurposing strategy was implemented to find the possible CYP1B1 inhibitors using machine learning (ML) and structure-based virtual screening (SB-VS) approaches. Initially, three different ML models were developed such as support vector machines (SVMs), random forest (RF), and artificial neural network (ANN); subsequently, the best-selected ML model was employed for virtual screening of the selleckchem database to identify potential CYP1B1 inhibitors. The inhibition potency of the obtained hits was judged by analyzing the crucial active site amino acid interactions against CYP1B1. After a thorough assessment of docking scores, binding affinities, as well as binding modes, four compounds were selected and further subjected to in vitro analysis. From the in vitro analysis, it was observed that chlorprothixene, nadifloxacin, and ticagrelor showed promising inhibitory activity toward CYP1B1 in the IC50 range of 0.07-3.00 μM. These new chemical scaffolds can be explored as adjuvant therapies to address CYP1B1-mediated drug-resistance problems.
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Affiliation(s)
- Baddipadige Raju
- Molecular
Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug
Research, Punjabi University, Patiala, Punjab 147002, India
| | - Gera Narendra
- Molecular
Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug
Research, Punjabi University, Patiala, Punjab 147002, India
| | - Himanshu Verma
- Molecular
Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug
Research, Punjabi University, Patiala, Punjab 147002, India
| | - Manoj Kumar
- Molecular
Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug
Research, Punjabi University, Patiala, Punjab 147002, India
| | - Bharti Sapra
- Molecular
Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug
Research, Punjabi University, Patiala, Punjab 147002, India
| | - Gurleen Kaur
- Center
for Basic and Translational Research in Health Sciences, Guru Nanak Dev University, Amritsar 143005, India
| | - Subheet Kumar jain
- Center
for Basic and Translational Research in Health Sciences, Guru Nanak Dev University, Amritsar 143005, India
| | - Om Silakari
- Molecular
Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug
Research, Punjabi University, Patiala, Punjab 147002, India
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5
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Alvarado YJ, Olivarez Y, Lossada C, Vera-Villalobos J, Paz JL, Vera E, Loroño M, Vivas A, Torres FJ, Jeffreys LN, Hurtado-León ML, González-Paz L. Interaction of the new inhibitor paxlovid (PF-07321332) and ivermectin with the monomer of the main protease SARS-CoV-2: A volumetric study based on molecular dynamics, elastic networks, classical thermodynamics and SPT. Comput Biol Chem 2022; 99:107692. [PMID: 35640480 PMCID: PMC9107165 DOI: 10.1016/j.compbiolchem.2022.107692] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 04/28/2022] [Accepted: 05/02/2022] [Indexed: 02/04/2023]
Abstract
The COVID-19 pandemic has accelerated the study of drugs, most notably ivermectin and more recently Paxlovid (PF-07321332) which is in phase III clinical trials with experimental data showing covalent binding to the viral protease Mpro. Theoretical developments of catalytic site-directed docking support thermodynamically feasible non-covalent binding to Mpro. Here we show that Paxlovid binds non-covalently at regions other than the catalytic sites with energies stronger than reported and at the same binding site as the ivermectin B1a homologue, all through theoretical methodologies, including blind docking. We volumetrically characterize the non-covalent interaction of the ivermectin homologues (avermectins B1a and B1b) and Paxlovid with the mMpro monomer, through molecular dynamics and scaled particle theory (SPT). Using the fluctuation-dissipation theorem (FDT), we estimated the electric dipole moment fluctuations at the surface of each of complex involved in this study, with similar trends to that observed in the interaction volume. Using fluctuations of the intrinsic volume and the number of flexible fragments of proteins using anisotropic and Gaussian elastic networks (ANM+GNM) suggests the complexes with ivermectin are more dynamic and flexible than the unbound monomer. In contrast, the binding of Paxlovid to mMpro shows that the mMpro-PF complex is the least structurally dynamic of all the species measured in this investigation. The results support a differential molecular mechanism of the ivermectin and PF homologues in the mMpro monomer. Finally, the results showed that Paxlovid despite beingbound in different sites through covalent or non-covalent forms behaves similarly in terms of its structural flexibility and volumetric behaviour.
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Affiliation(s)
- Ysaias José Alvarado
- Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Investigación y Tecnología de Materiales (CITeMA), Laboratorio de Caracterización Molecular y Biomolecular, 4001 Maracaibo, Bolivarian Republic of Venezuela,Corresponding author
| | - Yosmari Olivarez
- Universidad del Zulia (LUZ). Facultad Experimental de Ciencias (FEC), Departamento de Quimica, Laboratorio de Electronica Molecular, 4001 Maracaibo, Bolivarian Republic of Venezuela
| | - Carla Lossada
- Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Investigación y Tecnología de Materiales (CITeMA), Laboratorio de Caracterización Molecular y Biomolecular, 4001 Maracaibo, Bolivarian Republic of Venezuela
| | - Joan Vera-Villalobos
- Facultad de Ciencias Naturales y Matemáticas, Departamento de Química y Ciencias Ambientales, Laboratorio de Análisis Químico Instrumental (LAQUINS), Escuela Superior Politécnica del Litoral, Guayaquil, Ecuador
| | - José Luis Paz
- Departamento Académico de Química Inorgánica, Facultad de Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Eddy Vera
- Universidad del Zulia (LUZ). Facultad Experimental de Ciencias (FEC), Departamento de Quimica, Laboratorio de Electronica Molecular, 4001 Maracaibo, Bolivarian Republic of Venezuela
| | - Marcos Loroño
- Departamento Académico de Química Analítica e Instrumental, Facultad de Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Alejandro Vivas
- Universidad del Zulia (LUZ). Facultad Experimental de Ciencias (FEC), Departamento de Quimica, Laboratorio de Electronica Molecular, 4001 Maracaibo, Bolivarian Republic of Venezuela
| | - Fernando Javier Torres
- Grupo de Química Computacional y Teórica (QCT-UR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia,Grupo de Química Computacional y Teórica (QCT-USFQ), Instituto de Simulación Computacional (ISC-USFQ), Departamento de Ingeniería Química, Universidad San Francisco de Quito (USFQ), Quito, Ecuador
| | - Laura N. Jeffreys
- Centre for Drugs and Diagnostics, Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - María Laura Hurtado-León
- Universidad del Zulia (LUZ), Facultad Experimental de Ciencias (FEC), Departamento de Biología, Laboratorio de Genética y Biología Molecular (LGBM), Maracaibo 4001, Zulia, Bolivarian Republic of Venezuela
| | - Lenin González-Paz
- Universidad del Zulia (LUZ), Facultad Experimental de Ciencias (FEC), Departamento de Biología, Laboratorio de Genética y Biología Molecular (LGBM), Maracaibo 4001, Zulia, Bolivarian Republic of Venezuela,Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Estudios Botanicos y Agroforestales, (CEBA), Laboratorio de Proteccion Vegetal, 4001 Maracaibo, Bolivarian Republic of Venezuela,Corresponding author at: Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Estudios Botanicos y Agroforestales, (CEBA), Laboratorio de Proteccion Vegetal, 4001 Maracaibo, Bolivarian Republic of Venezuela
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6
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Gupta S, Singh V, Varadwaj PK, Chakravartty N, Katta AVSKM, Lekkala SP, Thomas G, Narasimhan S, Reddy AR, Reddy Lachagari VB. Secondary metabolites from spice and herbs as potential multitarget inhibitors of SARS-CoV-2 proteins. J Biomol Struct Dyn 2022; 40:2264-2283. [PMID: 33107812 PMCID: PMC7605658 DOI: 10.1080/07391102.2020.1837679] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 10/11/2020] [Indexed: 01/08/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been responsible for the current global pandemic that has caused a death toll of >1.12 million worldwide and number continues to climb in several countries. Currently, there are neither specific antiviral drugs nor vaccines for the treatment and prevention of COVID-19. We screened in silico, a group of natural spice and herbal secondary metabolites (SMs) for their inhibition efficacy against multiple target proteins of SARS-CoV-2 as well as the human angiotensin-converting enzyme 2 protein. Docking and simulation results indicated that epicatechin, embelin, hesperidin, cafestol, murrayanine and murrayaquinone-A have higher inhibition efficacy over at least one of the known antiviral drugs such as Hydroxychloroquine, Remdesivir and Ribavirin. Combination of these potentially effective SMs from their respective plant sources was analysed, and its absorption and acute oral toxicity were examined in Wistar rats and classified as category 5 as per the Globally Harmonized System. The identified SMs may be useful in the development of preventive nutraceuticals, food supplements and antiviral drugs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Vishal Singh
- Department of Applied Sciences, Indian Institute of Information Technology, Allahabad, India
| | - Pritish Kumar Varadwaj
- Department of Applied Sciences, Indian Institute of Information Technology, Allahabad, India
| | | | | | | | | | | | - Arjula R. Reddy
- Department of Plant Sciences, University of Hyderabad, Hyderabad, India
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7
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Stofberg ML, Caillet C, de Villiers M, Zininga T. Inhibitors of the Plasmodium falciparum Hsp90 towards Selective Antimalarial Drug Design: The Past, Present and Future. Cells 2021; 10:2849. [PMID: 34831072 PMCID: PMC8616389 DOI: 10.3390/cells10112849] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 12/12/2022] Open
Abstract
Malaria is still one of the major killer parasitic diseases in tropical settings, posing a public health threat. The development of antimalarial drug resistance is reversing the gains made in attempts to control the disease. The parasite leads a complex life cycle that has adapted to outwit almost all known antimalarial drugs to date, including the first line of treatment, artesunate. There is a high unmet need to develop new strategies and identify novel therapeutics to reverse antimalarial drug resistance development. Among the strategies, here we focus and discuss the merits of the development of antimalarials targeting the Heat shock protein 90 (Hsp90) due to the central role it plays in protein quality control.
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Affiliation(s)
| | | | | | - Tawanda Zininga
- Department of Biochemistry, Stellenbosch University, Stellenbosch 7600, South Africa; (M.L.S.); (C.C.); (M.d.V.)
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8
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Neumann J, Boknik P, Kirchhefer U, Gergs U. The role of PP5 and PP2C in cardiac health and disease. Cell Signal 2021; 85:110035. [PMID: 33964402 DOI: 10.1016/j.cellsig.2021.110035] [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: 01/05/2021] [Revised: 04/16/2021] [Accepted: 05/03/2021] [Indexed: 02/08/2023]
Abstract
Protein phosphatases are important, for example, as functional antagonists of β-adrenergic stimulation of the mammalian heart. While β-adrenergic stimulations increase the phosphorylation state of regulatory proteins and therefore force of contraction in the heart, these phosphorylations are reversed and thus force is reduced by the activity of protein phosphatases. In this context the role of PP5 and PP2C is starting to unravel. They do not belong to the same family of phosphatases with regard to sequence homology, many similarities with regard to location, activation by lipids and putative substrates have been worked out over the years. We also suggest which pathways for regulation of PP5 and/or PP2C described in other tissues and not yet in the heart might be useful to look for in cardiac tissue. Both phosphatases might play a role in signal transduction of sarcolemmal receptors in the heart. Expression of PP5 and PP2C can be increased by extracellular stimuli in the heart. Because PP5 is overexpressed in failing animal and human hearts, and because overexpression of PP5 or PP2C leads to cardiac hypertrophy and KO of PP5 leads to cardiac hypotrophy, one might argue for a role of PP5 and PP2C in heart failure. Because PP5 and PP2C can reduce, at least in vitro, the phosphorylation state of proteins thought to be relevant for cardiac arrhythmias, a role of these phosphatases for cardiac arrhythmias is also probable. Thus, PP5 and PP2C might be druggable targets to treat important cardiac diseases like heart failure, cardiac hypertrophy and cardiac arrhythmias.
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Affiliation(s)
- Joachim Neumann
- Institut für Pharmakologie und Toxikologie, Medizinische Fakultät, Martin-Luther-Universität Halle-Wittenberg, Magdeburger Str. 4, D-06097 Halle, Germany.
| | - Peter Boknik
- Institut für Pharmakologie und Toxikologie, Medizinische Fakultät, Westfälische Wilhelms-Universität, Domagkstraße 12, D-48149 Münster, Germany.
| | - Uwe Kirchhefer
- Institut für Pharmakologie und Toxikologie, Medizinische Fakultät, Westfälische Wilhelms-Universität, Domagkstraße 12, D-48149 Münster, Germany.
| | - Ulrich Gergs
- Institut für Pharmakologie und Toxikologie, Medizinische Fakultät, Martin-Luther-Universität Halle-Wittenberg, Magdeburger Str. 4, D-06097 Halle, Germany.
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9
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Raju B, Verma H, Narendra G, Sapra B, Silakari O. Multiple machine learning, molecular docking, and ADMET screening approach for identification of selective inhibitors of CYP1B1. J Biomol Struct Dyn 2021; 40:7975-7990. [PMID: 33769194 DOI: 10.1080/07391102.2021.1905552] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Cytochrome P4501B1 is a ubiquitous family protein that is majorly overexpressed in tumors and is responsible for biotransformation-based inactivation of anti-cancer drugs. This inactivation marks the cause of resistance to chemotherapeutics. In the present study, integrated in-silico approaches were utilized to identify selective CYP1B1 inhibitors. To achieve this objective, we initially developed different machine learning models corresponding to two isoforms of the CYP1 family i.e. CYP1A1 and CYP1B1. Subsequently, small molecule databases including ChemBridge, Maybridge, and natural compound library were screened from the selected models of CYP1B1 and CYP1A1. The obtained CYP1B1 inhibitors were further subjected to molecular docking and ADMET analysis. The selectivity of the obtained hits for CYP1B1 over the other isoforms was also judged with molecular docking analysis. Finally, two hits were found to be the most stable which retained key interactions within the active site of CYP1B1 after the molecular dynamics simulations. Novel compound with CYP-D9 and CYP-14 IDs were found to be the most selective CYP1B1 inhibitors which may address the issue of resistance. Moreover, these compounds can be considered as safe agents for further cell-based and animal model studies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Baddipadige Raju
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, India
| | - Himanshu Verma
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, India
| | - Gera Narendra
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, India
| | - Bharti Sapra
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, India
| | - Om Silakari
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, India
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10
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Kumar N, Gorai B, Gupta S, Shiva, Goel N. Extrapolation of hydroxytyrosol and its analogues as potential anti-inflammatory agents. J Biomol Struct Dyn 2020; 39:5588-5599. [PMID: 32672527 DOI: 10.1080/07391102.2020.1792990] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Discovery of potential lead molecule is a challenging, and complex process which require lots of money, patience, and manpower. Human beings are using natural products, predominantly secondary metabolites, for this purpose since ancient time and they are still working on them as a potent source for drug discovery due to their wide structural diversity. Phenolic phytochemicals such as hydroxytyrosol and tyrosol are natural antioxidant and involved in many biological disease cure. Herein, we have carried out the quantum chemical calculations for conformational analysis, geometry optimization and computation of electronic as well as optical properties of hydroxytyrosol and its analogues (1a-1k) in terms of density functional theory by using Gaussian 09 program suite. The eventual charge transfer within the molecules has been confirmed by the analysis of frontier molecular orbitals. The molecular docking studies of 1a-1k with cyclooxygenase-2 showed the noticeable binding affinity as compared to other nonsteroidal anti-inflammatory drugs viz. aspirin, naproxen and celecoxib. Computation of pharmacokinetics and pharmacological properties confirmed the lead/drug like potential of these screened molecules. Furthermore, the molecular dynamics simulation of best three docked ligands (1f, 1h and 1k)-receptor complex and their binding free energy calculations reveals that these molecules bind in the catalytic cavity of cyclooxygenase-2 and found stable during the 100 ns of simulation. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Naresh Kumar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Madhya Pradesh, India
| | - Biswajit Gorai
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore, India
| | - Saurabh Gupta
- AgriGenome labs Pvt. Ltd. SINC, IKP Knowledge Park, Genome Valley, Hyderabad, India
| | - Shiva
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Nidhi Goel
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, India
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11
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Boonkaew T, Mongkol W, Prasert S, Paochan P, Yoneda S, Nguitragool W, Kumpitak C, Sattabongkot J, Kubera A. Transcriptome analysis of Anopheles dirus and Plasmodium vivax at ookinete and oocyst stages. Acta Trop 2020; 207:105502. [PMID: 32320680 DOI: 10.1016/j.actatropica.2020.105502] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 04/15/2020] [Accepted: 04/15/2020] [Indexed: 02/07/2023]
Abstract
Malaria is transmitted by Plasmodium parasites through the bite of female Anopheles mosquitoes. One of the most important mosquito vectors in the Greater Mekong Subregion is Anopheles dirus. This study reports RNA sequencing (RNA-Seq) transcriptome analysis of An. dirus at 18 hours and 7 days after a P. vivax-infected blood meal, which represent infection at the ookinete and oocyst parasite developmental stages, respectively. Following infection, 582 An. dirus transcripts were modulated. The 2,408 P. vivax transcripts could be classified into ookinete-specific, two-stage, and oocyst-specific groups. Results were validated by quantitative reverse transcription polymerase chain reaction. Gene ontology analysis of the vector and parasite revealed several biological pathways for both, providing a better understanding of Anopheles-Plasmodium interactions at the ookinete and oocyst stages.
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Affiliation(s)
- Tippawan Boonkaew
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Watcharakorn Mongkol
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Sureerat Prasert
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Pattaweeya Paochan
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Saki Yoneda
- Department of Biotechnology, Graduate school of Engineering, Osaka University, Japan
| | - Wang Nguitragool
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Chalermpon Kumpitak
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Jetsumon Sattabongkot
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Anchanee Kubera
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand; Centre for Advanced Studies in Tropical Natural Resources, Kasetsart University, Bangkok, 10900, Thailand.
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12
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Zhu Y, Gao Y, Sun X, Wang C, Rui X, Si D, Zhu J, Li W, Liu J. Discovery of novel serine/threonine protein phosphatase 1 inhibitors from traditional Chinese medicine through virtual screening and biological assays. J Biomol Struct Dyn 2019; 38:5464-5473. [PMID: 31820681 DOI: 10.1080/07391102.2019.1702588] [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: 02/07/2023]
Abstract
Protein phosphatase 1 (PP1) is a critical regulator of several processes, such as muscle contraction, neuronal signaling, glycogen synthesis, and cell proliferation. Dysregulation of PP1 has recently been found to be implicated in cardiac dysfunctions, which indicates that PP1 could be an attractive therapeutic target. However, discovery of PP1 inhibitors with satisfied safety and efficiency is still a challenge. Here, in order to discover potential PP1 inhibitors, compounds extracted from traditional Chinese medicine (TCM) were screened by a novel integrated virtual screening protocol including pharmacophore modeling and docking approaches. Combined with protein phosphatase inhibition assay, ZINC43060554 showed strongly inhibitory activity with IC50 values of 26.78 μM. Furthermore, molecular dynamics simulation and Molecular Mechanics/Generalized Born Surface Area binding free-energy analysis were performed to examine the stability of ligand binding modes. These novel scaffolds discovered in the present study can be used for rational design of PP1 inhibitors with high affinity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yehua Zhu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China.,Research Institute, Nanjing Tongrentang Pharmaceutical Co. Ltd, Nanjing, China
| | - Yi Gao
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Xinjie Sun
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Chao Wang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Xiyan Rui
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Dongjuan Si
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Junru Zhu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Wei Li
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China.,Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, Jiangsu, China.,Jiangsu Key Laboratory for Functional Substances of Chinese Medicine, Stake Key Laboratory Cultivation Base for TCM Quality and Efficacy, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jian Liu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China.,Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, Jiangsu, China.,Jiangsu Key Laboratory for Functional Substances of Chinese Medicine, Stake Key Laboratory Cultivation Base for TCM Quality and Efficacy, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
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13
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Deciphering the transcriptomic insight during organogenesis in Castor ( Ricinus communis L.), Jatropha ( Jatropha curcas L.) and Sunflower ( Helianthus annuus L.). 3 Biotech 2019; 9:434. [PMID: 31696039 DOI: 10.1007/s13205-019-1960-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 10/18/2019] [Indexed: 10/25/2022] Open
Abstract
Cultivation of the castor crop is hindered by various factors and one of the approaches for genetic improvement of the crop is through exploitation of biotechnological tools. Response of castor tissues to in vitro culture is poor which necessitated this study on understanding the molecular basis of organogenesis in cultured tissues of castor, through de novo transcriptome analysis and by comparing with jatropha and sunflower having good regeneration ability. Transcriptome profiling analysis was carried out with hypocotyl explants from castor, jatropha and cotyledons from sunflower cultured on MS media supplemented with different concentrations of hormones. Differentially expressed genes during dedifferentiation and organogenic differentiation stages of callus included components of auxin and cytokinin signaling, secondary metabolite synthesis, genes encoding transcription factors, receptor kinases and protein kinases. In castor, many genes involved in auxin biosynthesis and homeostasis like WAT1, vacuolar transporter genes, transcription factors like short root like protein were down-regulated while genes like DELLA were up-regulated accounting for regeneration recalcitrance. Validation of 62 DEGs through qRT-PCR showed a consensus of 77.4% of the genes expressed. Overall study provides set of genes involved in the process of organogenesis in three oilseed crops which forms a basis for understanding and improving the efficiency of plant regeneration and genetic transformation in castor.
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14
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Gupta S, Mishra VK, Kumari S, Raavi, Chand R, Varadwaj PK. Deciphering genome-wide WRKY gene family of Triticum aestivum L. and their functional role in response to Abiotic stress. Genes Genomics 2018; 41:79-94. [PMID: 30238225 DOI: 10.1007/s13258-018-0742-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 09/11/2018] [Indexed: 12/18/2022]
Abstract
WRKY transcription factors (TFs) act in regulating plant growth and development as well as in response to different stress. Some earlier studies done by individual researchers reported different wheat WRKY TFs. Although, the recently released wheat genome has opened an avenue to investigate wheat WRKYs (TaWRKY) TFs. Prime objective of this study to performed genome-wide classifications of TaWRKYs and their functional annotation. The classification of 107 individual identified characterized sequences of TaWRKY (IICS-TaWRKY) and 160 uncharacterized draft sequences of TaWRKY (UDS-TaWRKY), along with their gene structures and motifs analysis was performed. Along with comparative sequence analysis and microarray analysis was performed to mimic out TaWRKYs functions in response to different abiotic stresses, accompanied by in-vitro validation. The comparative phylogenetic analysis and estimation of Ka/Ks ratio with Triticum urartu, illustrate group based clasifications of TaWRKYs and evolutionary divergences. Furthermore, motif-based and protein-DNA interaction analysis of TaWRKYs helps to identify, their putative function in target DNA recognition sites. Subsequently, results of microarray and comparative sequence analysis provides the evidence of TaWRKYs involved in heat and/or drought stress. Further, in-vitro results validates that TaWRKY014, TaWRKY090 are found to participate in response of drought stress, whereas TaWRKY008, TaWRKY122, and WRKY45 are involved in response of heat and drought stress. These findings can be utilized in developing novel heat and drought-tolerant wheat cultivars using marker-assisted breeding and transgenic development.
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Affiliation(s)
- Saurabh Gupta
- Department of Applied Sciences, Indian Institute of Information Technology, Deoghat, Jhalwa, Allahabad, 211015, India.,AgriGenome Labs Pvt. Ltd., Hyderabad, 500078, India
| | - Vinod Kumar Mishra
- Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, 221005, India
| | - Sunita Kumari
- Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, 221005, India
| | - Raavi
- Molecular Biology, Cell Biology and Biochemistry Program, Boston University, Boston, 02215, USA
| | - Ramesh Chand
- Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, 221005, India
| | - Pritish Kumar Varadwaj
- Department of Applied Sciences, Indian Institute of Information Technology, Deoghat, Jhalwa, Allahabad, 211015, India.
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15
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Gupta S, Gupta V, Singh V, Varadwaj PK. Extrapolation of significant genes and transcriptional regulatory networks involved in Zea mays in response in UV-B stress. Genes Genomics 2018; 40:973-990. [PMID: 30155715 DOI: 10.1007/s13258-018-0705-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 05/06/2018] [Indexed: 12/21/2022]
Abstract
A wide range of plant species growth influenced when they exposed to solar UV-B radiation. Leaves of the plant are highly affected by UV-B radiation lead to the reduction in the growth of the plant. Current work demonstrates the comparative transcriptional changes and visible symptoms occurred in the maize leaf growth zone (GZ). Primary objective of this study was to identify differentially expressed genes (DEGs) responsible for leaf growth and their association in the transcriptional regulatory network under UV-B stress. Whole transcriptomic data was analysed and the quality check was tested for each sample and further genome-wide mapping and DEGs were performed. Gene Ontology (GO) based functional annotation, associated transcriptional networks and molecular pathways were annotated. Reduction in cell production due to UV-B stress causes a decrease in leaf's length and size was observed. Further, the specific role of the DEGs, in UV-B signalling pathways and other molecular functions responsible for leaf cell death was discovered. Results also infer that the major changes occurred in the cell cycle, transcriptional regulation, post-transcriptional modification, phytohormones, flavonoids biosynthesis, and chromatin remodeling. UV-B signalling pathways and the transcriptional regulatory networks infer the different molecular steps along with downstream transcriptional and post-transcriptional control of metabolic enzymes used in long-term memory adoption and attainment resistance to UV-B stress identified. Effects of UV-B radiation on leaf growth was noted in this study. UV-B stress response genes and associated transcriptional regulatory networks were identified, can be used in developing the marker assist UB-B stress tolerant genotypes of the maize.
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Affiliation(s)
- Saurabh Gupta
- Department of Bioinformatics, Indian Institute of Information Technology-Allahabad, Devghat, Jhalwa, Allahabad, UP, 211015, India
| | - Vikas Gupta
- Department of Molecular and Cellular Engineering, JIBB, Sam Higginbottom University of Agriculture, Technology and Sciences, Allahabad, 211007, India
| | - Vishal Singh
- Department of Bioinformatics, Indian Institute of Information Technology-Allahabad, Devghat, Jhalwa, Allahabad, UP, 211015, India
| | - Pritish Kumar Varadwaj
- Department of Bioinformatics, Indian Institute of Information Technology-Allahabad, Devghat, Jhalwa, Allahabad, UP, 211015, India.
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16
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Iglesias J, Saen‐oon S, Soliva R, Guallar V. Computational structure‐based drug design: Predicting target flexibility. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2018. [DOI: 10.1002/wcms.1367] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
| | | | | | - Victor Guallar
- Life Science DepartmentBarcelonaSpain
- ICREA, Passeig Lluís Companys 23BarcelonaSpain
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17
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Kumar A, Srivastava G, Negi AS, Sharma A. Docking, molecular dynamics, binding energy-MM-PBSA studies of naphthofuran derivatives to identify potential dual inhibitors against BACE-1 and GSK-3β. J Biomol Struct Dyn 2018; 37:275-290. [DOI: 10.1080/07391102.2018.1426043] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Akhil Kumar
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow 226015, Uttar Pradesh, India
| | - Gaurava Srivastava
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow 226015, Uttar Pradesh, India
| | - Arvind S. Negi
- Chemical Sciences Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow 226015, Uttar Pradesh, India
| | - Ashok Sharma
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow 226015, Uttar Pradesh, India
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18
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Zhou H, Wang C, Deng T, Tao R, Li W. Novel urushiol derivatives as HDAC8 inhibitors: rational design, virtual screening, molecular docking and molecular dynamics studies. J Biomol Struct Dyn 2017. [DOI: 10.1080/07391102.2017.1344568] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Hao Zhou
- Key Lab of Biomass Energy and Material, Nanjing, Jiangsu 210042, China
- Institute of Chemical Industry of Forest Products, CAF, Nanjing, Jiangsu 210042, China
| | - Chengzhang Wang
- Key Lab of Biomass Energy and Material, Nanjing, Jiangsu 210042, China
- Institute of Chemical Industry of Forest Products, CAF, Nanjing, Jiangsu 210042, China
| | - Tao Deng
- Institute of Chemical Industry of Forest Products, CAF, Nanjing, Jiangsu 210042, China
| | - Ran Tao
- Institute of Chemical Industry of Forest Products, CAF, Nanjing, Jiangsu 210042, China
| | - Wenjun Li
- Institute of Chemical Industry of Forest Products, CAF, Nanjing, Jiangsu 210042, China
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19
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Identification and characterization of a grain micronutrient-related OsFRO2 rice gene ortholog from micronutrient-rich little millet (Panicum sumatrense). 3 Biotech 2017; 7:80. [PMID: 28500402 DOI: 10.1007/s13205-017-0656-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 02/13/2017] [Indexed: 12/15/2022] Open
Abstract
Minor millets are considered as nutrient-rich cereals having significant effect in improving human health. In this study, a rice ortholog of Ferric Chelate Reductase (FRO2) gene involved in plant metal uptake has been identified in iron-rich Little millet (LM) using PCR and next generation sequencing-based strategy. FRO2 gene-specific primers designed from rice genome amplified 2.7 Kb fragment in LM genotype RLM-37. Computational genomics analyses of the sequenced amplicon showed high level sequence similarity with rice OsFRO2 gene. The predicted gene structure showed the presence of 6 exons and 5 introns and its protein sequence was found to contain ferric reductase and NOX_Duox_Like_FAD_NADP domains. Further, 3D structure analysis of FCR-LM model protein (494 amino acids) shows that it has 18 helices, 10 beta sheets, 10 strands, 41 beta turn and 5 gamma turn with slight deviation from the FCR-Os structure. Besides, the structures of FCR-LM and FCR-Os were modelled followed by molecular dynamics simulations. The overall study revealed both sequence and structural similarity between the identified gene and OsFRO2. Thus, a putative ferric chelate reductase gene has been identified in LM paving the way for using this approach for identification of orthologs of other metal genes from millets. This also facilitates mining of effective alleles of known genes for improvement of staple crops like rice.
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20
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Genome-wide analysis of miRNAs and Tasi-RNAs in Zea mays in response to phosphate deficiency. Funct Integr Genomics 2017; 17:335-351. [PMID: 28070736 DOI: 10.1007/s10142-016-0538-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 11/28/2016] [Accepted: 12/05/2016] [Indexed: 12/12/2022]
Abstract
Globally important cereal crop maize provides important nutritions and starch in dietary foods. Low phosphate (LPi) availability in the soil frequently limits the maize quality and yield across the world. Small non-coding RNAs (Snc-RNAs) play crucial roles in growth and adaptation of plants to the environment. Snc-RNAs like microRNAs (miRs) and trans-acting small interfering RNAs (Tasi-Rs) play important functions in posttranscriptional regulation of gene expression, which controls plant development, reproduction, and biotic/abiotic stress responses. In order to identify the miR and Tasi-R alterations in leaf and root of maize in response to sufficient phosphate and LPi at 3LS and 4LS, the snc-RNA population libraries for 0th, 1st, 2nd, 4th, and 8th day were constructed. These libraries were used for genome-wide alignment and RNA-fold analysis for possible prediction of potential miRs and Tasi-Rs. This study reported 174 known and conserved differentially expressed miRs of 27 miR families of maize plant. In addition, leaf and root specific potential novel miRs representing 155 new families were also discovered. Differentially expressed conserved as well as novel miR functions in root and leaf during early stage of Pi starvation were extensively discussed. Leaf and root specific miRs as well as common miRs with their target genes, participating in different biological, cellular, and metabolic processes were explored. Further, four miR390-directed Tasi-Rs which belong to TAS3 gene family along with other orthologs of Tasi-Rs were also identified. Finally, the study provides an insight into the composite regulatory mechanism of miRs in maize in response to Pi deficiency.
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21
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Batra R, Saripalli G, Mohan A, Gupta S, Gill KS, Varadwaj PK, Balyan HS, Gupta PK. Comparative Analysis of AGPase Genes and Encoded Proteins in Eight Monocots and Three Dicots with Emphasis on Wheat. FRONTIERS IN PLANT SCIENCE 2017; 8:19. [PMID: 28174576 PMCID: PMC5259687 DOI: 10.3389/fpls.2017.00019] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 01/04/2017] [Indexed: 05/11/2023]
Abstract
ADP-glucose pyrophosphorylase (AGPase) is a heterotetrameric enzyme with two large subunits (LS) and two small subunits (SS). It plays a critical role in starch biosynthesis. We are reporting here detailed structure, function and evolution of the genes encoding the LS and the SS among monocots and dicots. "True" orthologs of maize Sh2 (AGPase LS) and Bt2 (AGPase SS) were identified in seven other monocots and three dicots; structure of the enzyme at protein level was also studied. Novel findings of the current study include the following: (i) at the DNA level, the genes controlling the SS are more conserved than those controlling the LS; the variation in both is mainly due to intron number, intron length and intron phase distribution; (ii) at protein level, the SS genes are more conserved relative to those for LS; (iii) "QTCL" motif present in SS showed evolutionary differences in AGPase belonging to wheat 7BS, T. urartu, rice and sorghum, while "LGGG" motif in LS was present in all species except T. urartu and chickpea; SS provides thermostability to AGPase, while LS is involved in regulation of AGPase activity; (iv) heterotetrameric structure of AGPase was predicted and analyzed in real time environment through molecular dynamics simulation for all the species; (v) several cis-acting regulatory elements were identified in the AGPase promoters with their possible role in regulating spatial and temporal expression (endosperm and leaf tissue) and also the expression, in response to abiotic stresses; and (vi) expression analysis revealed downregulation of both subunits under conditions of heat and drought stress. The results of the present study have allowed better understanding of structure and evolution of the genes and the encoded proteins and provided clues for exploitation of variability in these genes for engineering thermostable AGPase.
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Affiliation(s)
- Ritu Batra
- Bioinformatics Infrastructure Facility (BIF) Laboratory, Department of Genetics and Plant Breeding, Ch. Charan Singh UniversityMeerut, India
| | - Gautam Saripalli
- Molecular Biology Laboratory, Department of Genetics and Plant Breeding, Ch. Charan Singh UniversityMeerut, India
| | - Amita Mohan
- Department of Crop and Soil Sciences, Washington State UniversityPullman, WA, USA
| | - Saurabh Gupta
- Department of Bioinformatics, Indian Institute of Information Technology-AllahabadAllahabad, India
| | - Kulvinder S. Gill
- Department of Crop and Soil Sciences, Washington State UniversityPullman, WA, USA
- *Correspondence: Kulvinder S. Gill
| | - Pritish K. Varadwaj
- Department of Bioinformatics, Indian Institute of Information Technology-AllahabadAllahabad, India
| | - Harindra S. Balyan
- Bioinformatics Infrastructure Facility (BIF) Laboratory, Department of Genetics and Plant Breeding, Ch. Charan Singh UniversityMeerut, India
- Molecular Biology Laboratory, Department of Genetics and Plant Breeding, Ch. Charan Singh UniversityMeerut, India
| | - Pushpendra K. Gupta
- Bioinformatics Infrastructure Facility (BIF) Laboratory, Department of Genetics and Plant Breeding, Ch. Charan Singh UniversityMeerut, India
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22
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Gupta S, Yadav BS, Raj U, Freilich S, Varadwaj PK. Transcriptomic Analysis of Soil Grown T. aestivum cv. Root to Reveal the Changes in Expression of Genes in Response to Multiple Nutrients Deficiency. FRONTIERS IN PLANT SCIENCE 2017; 8:1025. [PMID: 28690617 PMCID: PMC5479913 DOI: 10.3389/fpls.2017.01025] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 05/29/2017] [Indexed: 05/11/2023]
Abstract
Deficiency of necessary macronutrients, i.e., Potassium (K), Magnesium (Mg), Nitrogen (N), Phosphorus (P), and Sulfate (S) in the soil leads to a reduction in plant growth and yield, which is a result of changes in expression level of various genes. This study was performed to identify the differentially expressed genes and its associated metabolic pathways occurred in soil grown wheat root samples excavated from the control and treated fields. To identify the difference in gene expression levels due to deficiency of the said nutrients, a transcriptomic, meta-analysis was performed on array expression profile data. A set of 435 statistically significant probes encoding 398 Nutrient Deficiency Response Genes (NRGs) responding at-least one nutrients deficiency (ND) were identified. Out of them 55 NRGs were found to response to minimum two ND. Singular Enrichment Analysis (SEA) predicts ontological based classifications and functional analysis of NRGs in different cellular/molecular pathways involved in root development and growth. Functional annotation and reaction mechanism of differentially expressed genes, proteins/enzymes in the different metabolic pathway through MapMan analysis were explored. Further the meta-analysis was performed to revels the active involvement each NRGs in distinct tissues and their comparative potential expression analysis in different stress conditions. The study results in exploring the role of major acting candidate genes such as Non-specific serine/threonine protein kinase, Xyloglucan endotransglucosylase/hydrolase, Peroxides, Glycerophosphoryl diester phosphodiesterase, S-adenosylmethionine decarboxylase proenzyme, Dehydrin family proteins, Transcription factors, Membrane Proteins, Metal binding proteins, Photosystem proteins, Transporter and Transferase associated in different metabolic pathways. Finally, the differences of transcriptional responses in the soil-grown root of T. aestivum cv. and in-vitro grown model plants under nutrients deficiency were summarized.
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Affiliation(s)
- Saurabh Gupta
- Department of Bioinformatics, Indian Institute of Information TechnologyAllahabad, Allahabad, India
| | - Brijesh S. Yadav
- Department of Molecular Biology and Ecology of Plants, Tel Aviv UniversityTel Aviv, Israel
| | - Utkarsh Raj
- Department of Bioinformatics, Indian Institute of Information TechnologyAllahabad, Allahabad, India
| | - Shiri Freilich
- Institute of Plant Sciences, Newe Ya'ar Research Center, Agricultural Research OrganizationRamat Yishay, Israel
| | - Pritish K. Varadwaj
- Department of Bioinformatics, Indian Institute of Information TechnologyAllahabad, Allahabad, India
- *Correspondence: Pritish K. Varadwaj
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23
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Musyoka TM, Kanzi AM, Lobb KA, Bishop ÖT. Analysis of non-peptidic compounds as potential malarial inhibitors against Plasmodial cysteine proteases via integrated virtual screening workflow. J Biomol Struct Dyn 2016; 34:2084-101. [PMID: 26471975 PMCID: PMC5035544 DOI: 10.1080/07391102.2015.1108231] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 10/08/2015] [Indexed: 10/22/2022]
Abstract
Falcipain-2 (FP-2) and falcipain-3 (FP-3), haemoglobin-degrading enzymes in Plasmodium falciparum, are validated drug targets for the development of effective inhibitors against malaria. However, no commercial drug-targeting falcipains has been developed despite their central role in the life cycle of the parasites. In this work, in silico approaches are used to identify key structural elements that control the binding and selectivity of a diverse set of non-peptidic compounds onto FP-2, FP-3 and homologues from other Plasmodium species as well as human cathepsins. Hotspot residues and the underlying non-covalent interactions, important for the binding of ligands, are identified by interaction fingerprint analysis between the proteases and 2-cyanopyridine derivatives (best hits). It is observed that the size and chemical type of substituent groups within 2-cyanopyridine derivatives determine the strength of protein-ligand interactions. This research presents novel results that can further be exploited in the structure-based molecular-guided design of more potent antimalarial drugs.
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Affiliation(s)
- Thommas M. Musyoka
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
| | - Aquillah M. Kanzi
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
| | - Kevin A. Lobb
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
- Department of Chemistry, Rhodes University, Grahamstown, South Africa
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
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24
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Sit KC, van Lonkhuyzen D, Walsh T, Croll T. Prediction of a novel internal rearrangement of the insulin receptor. J Biomol Struct Dyn 2016; 35:857-867. [PMID: 27137342 DOI: 10.1080/07391102.2016.1165631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The insulin receptor (IR) plays critical roles in metabolism and growth, directed by the binding of insulin. Decades of research to understand the mechanism of insulin binding and activation of the IR have identified a region of the receptor, the C-terminal (CT) peptide, to be crucial for insulin binding. In particular, a truncated IR consisting of the first three domains fused to the CT peptide was found to bind insulin with nanomolar affinity, with undetectable binding in the absence of fused or soluble CT peptide. Problematically, all current crystal structures of the IR indicate the fusion point of the CT peptide to the three domains is located far from the position of the CT peptide as resolved in such structures. We have attempted to address this problem using molecular modelling and dynamics simulations. The results led to the identification of a potential inter-domain interaction between the L2 domain and the CT peptide that is not observed in any of the crystal structures of the IR. Investigations into this new interaction found a conformational change that could potentially be in response to insulin binding. Additionally, further simulation work with the new conformation demonstrated its compatibility with the position and orientation of insulin from the latest insulin-bound IR crystal structure.
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Affiliation(s)
- Kei C Sit
- a Institute of Health and Biomedical Innovation , Queensland University of Technology , Brisbane , Australia
| | - Derek van Lonkhuyzen
- a Institute of Health and Biomedical Innovation , Queensland University of Technology , Brisbane , Australia
| | - Terry Walsh
- b Faculty of Health, School of Biomedical Science , Institute of Health and Biomedical Innovation, Queensland University of Technology , Brisbane , QLD , Australia
| | - Tristan Croll
- a Institute of Health and Biomedical Innovation , Queensland University of Technology , Brisbane , Australia.,b Faculty of Health, School of Biomedical Science , Institute of Health and Biomedical Innovation, Queensland University of Technology , Brisbane , QLD , Australia
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Soni R, Sharma D, Patel S, Sharma B, Bhatt TK. Structure-based binding between protein farnesyl transferase and PRL-PTP of malaria parasite: an interaction study of prenylation process in Plasmodium. J Biomol Struct Dyn 2016; 34:2667-2678. [PMID: 26727035 DOI: 10.1080/07391102.2015.1126533] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Protein prenylation is a post-translational modification critical for many cellular processes such as DNA replication, signaling, and trafficking. It is mediated by protein farnesyltransferase by recognizing 'CAAX' motif on protein substrate. Plasmodium falciparum also possesses many such proteins with 'CAAX' motif, involved in various pathways of the parasite. The interaction studies of PfPFT with its substrate were carried out using synthetic peptides but not with full protein. Therefore, in this study, we have modeled both PfPFT and its substrate protein tyrosine phosphatase (PfPRL-PTP) followed by interaction studies using protein-protein docking and molecular dynamics simulation. Our findings provided a clear picture of interactions at atomic level between prenyltransferase and its protein substrate. We are assured that this piece of information can be extended to many other proteins of parasite containing 'CAAX' motif and that it may also lead to the development of anti-malarials based on the inhibition of prenylation-dependent pathways of parasite..
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Affiliation(s)
- Rani Soni
- a Department of Biotechnology , Central University of Rajasthan , NH-8, Bandarsindri , Rajasthan 305801 , India
| | - Drista Sharma
- a Department of Biotechnology , Central University of Rajasthan , NH-8, Bandarsindri , Rajasthan 305801 , India
| | - Sachin Patel
- a Department of Biotechnology , Central University of Rajasthan , NH-8, Bandarsindri , Rajasthan 305801 , India
| | - Bhaskar Sharma
- a Department of Biotechnology , Central University of Rajasthan , NH-8, Bandarsindri , Rajasthan 305801 , India
| | - Tarun Kumar Bhatt
- a Department of Biotechnology , Central University of Rajasthan , NH-8, Bandarsindri , Rajasthan 305801 , India
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Raj U, Kumar H, Gupta S, Varadwaj PK. Exploring dual inhibitors for STAT1 and STAT5 receptors utilizing virtual screening and dynamics simulation validation. J Biomol Struct Dyn 2015; 34:2115-29. [PMID: 26471877 DOI: 10.1080/07391102.2015.1108870] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Signal transducer and activator of transcription (STAT) proteins are latent cytoplasmic transcription factors that transduce signals from cytokines and growth factors to the nucleus and thereby regulate the expression of a variety of target genes. Although mutations of STATs have not been reported in human tumors but the activity of several members of the family, such as STAT1 and STAT5, is deregulated in a variety of human carcinoma. STAT1 and STAT5 share a structural similarity with a highly conserved SH2 domain which is responsible for the activation of STAT proteins on interaction with phosphotyrosine motifs for specific STAT-receptor contacts and STAT dimerization. The purpose of this study is to identify domain-specific dual inhibitors for both STAT1 and STAT5 proteins from a database of natural products and natural product-like compounds comprising of over 90,000 compounds. Virtual screening-based molecular docking was performed in order to find novel natural dual inhibitors. Further, the study was supported by the 50-ns molecular dynamics simulation for receptor-ligand complexes (STAT1-STOCK-1N-69677 and STAT5-STOCK-1N-69677). Analysis of molecular interactions in the SH2 domains of both STAT1 and STAT5 proteins with the ligand revealed few conserved amino acid residues which are responsible to stabilize the ligands within the binding pocket through bonded and non-bonded interactions. This study suggested that compound STOCK-1N-69677 might putatively act as a dual inhibitor of STAT1 and STAT5 receptors, through its binding to the SH2 domain.
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Affiliation(s)
- Utkarsh Raj
- a Department of Bioinformatics , Indian Institute of Information Technology-Allahabad , CC2-4203, Jhalwa Campus, Deoghat, Allahabad , Uttar Pradesh 211012 , India
| | - Himansu Kumar
- a Department of Bioinformatics , Indian Institute of Information Technology-Allahabad , CC2-4203, Jhalwa Campus, Deoghat, Allahabad , Uttar Pradesh 211012 , India
| | - Saurabh Gupta
- a Department of Bioinformatics , Indian Institute of Information Technology-Allahabad , CC2-4203, Jhalwa Campus, Deoghat, Allahabad , Uttar Pradesh 211012 , India
| | - Pritish Kumar Varadwaj
- a Department of Bioinformatics , Indian Institute of Information Technology-Allahabad , CC2-4203, Jhalwa Campus, Deoghat, Allahabad , Uttar Pradesh 211012 , India
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Nanda Kumar Y, Jeyakodi G, Gunasekaran K, Jambulingam P. Computational screening and characterization of putative vaccine candidates of Plasmodium vivax. J Biomol Struct Dyn 2015; 34:1736-50. [PMID: 26338678 DOI: 10.1080/07391102.2015.1090344] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Plasmodium vivax is the most prevalent species of malaria affecting millions of people annually worldwide and demands effective interventions to develop a successful vaccine. In this milieu, we have dedicated noteworthy efforts to characterize the proteome of P. vivax to give a lead for the epitope-based vaccine development. Membrane proteins of P. vivax were collected from SWISS PROT database and 10 antigenic proteins were identified among them by in silico analysis using multiple servers. T-cell and B-cell epitopes were identified and their immunity was assessed. Their ability to trigger humoral and cell-mediated responses was determined. Three dimensional models were constructed for the antigenic proteins using Modeller, Phyre2, and Modloop tools and their quality was validated using PROCHECK and ProSA-web validation servers. Further, the binding affinity and molecular interactions of these antigenic proteins were characterized by performing protein-protein docking against transmission-blocking anti-malaria antibody Fab2A8 (PDB ID: 3S62) using Z-dock module of Discovery Studio 4.0. The presence of potential B & T-cell epitopes, major histocompatibility complex-binding sites, and their efficient interactions with Fab2A8 antibody suggests the use of predicted antigenic proteins for the construction of multi-epitope peptide vaccine against P. vivax.
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Affiliation(s)
- Y Nanda Kumar
- a Biomedical Informatics Centre, Vector Control Research Centre , Indian Council of Medical Research , Pondicherry 605006 , India
| | - G Jeyakodi
- a Biomedical Informatics Centre, Vector Control Research Centre , Indian Council of Medical Research , Pondicherry 605006 , India
| | - K Gunasekaran
- a Biomedical Informatics Centre, Vector Control Research Centre , Indian Council of Medical Research , Pondicherry 605006 , India
| | - P Jambulingam
- a Biomedical Informatics Centre, Vector Control Research Centre , Indian Council of Medical Research , Pondicherry 605006 , India
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Hasan MA, Mazumder MHH, Chowdhury AS, Datta A, Khan MA. Molecular-docking study of malaria drug target enzyme transketolase in Plasmodium falciparum 3D7 portends the novel approach to its treatment. SOURCE CODE FOR BIOLOGY AND MEDICINE 2015; 10:7. [PMID: 26089981 PMCID: PMC4472393 DOI: 10.1186/s13029-015-0037-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Accepted: 05/08/2015] [Indexed: 01/17/2023]
Abstract
BACKGROUND Malaria has been a major life threatening mosquito borne disease from long since. Unavailability of any effective vaccine and recent emergence of multi drug resistant strains of malaria pathogen Plasmodium falciparum continues to cause persistent deaths in the tropical and sub-tropical region. As a result, demands for new targets for more effective anti-malarial drugs are escalating. Transketolase is an enzyme of the pentose phosphate pathway; a novel pathway which is involved in energy generation and nucleic acid synthesis. Moreover, significant difference in homology between Plasmodium falciparum transketolase (Pftk) and human (Homo sapiens) transketolase makes it a suitable candidate for drug therapy. Our present study is aimed to predict the 3D structure of Plasmodium falciparum transketolase and design an inhibitor against it. RESULTS The primary and secondary structural features of the protein is calculated by ProtParam and SOPMA respectively which revealed the protein is composed of 43.3 % alpha helix and 33.04 % random coils along with 15.62 % extended strands, 8.04 % beta turns. The three dimensional structure of the transketolase is constructed using homology modeling tool MODELLAR utilizing several available transketolase structures as templates. The structure is then subjected to deep optimization and validated by structure validation tools PROCHECK, VERIFY 3D, ERRAT, QMEAN. The predicted model scored 0.74 for global model reliability in PROCHECK analysis, which ensures the quality of the model. According to VERIFY 3D the predicted model scored 0.77 which determines good environmental profile along with ERRAT score of 78.313 which is below 95 % rejection limit. Protein-protein and residue-residue interaction networks are generated by STRING and RING server respectively. CASTp server was used to analyze active sites and His 109, Asn 108 and His 515 are found to be more positive site to dock the substrate, in addition molecular docking simulation with Autodock vina determined the estimated free energy of molecular binding was of -6.6 kcal/mol for most favorable binding of 6'-Methyl-Thiamin Diphosphate. CONCLUSION This predicted structure of Pftk will serve first hand in the future development of effective Pftk inhibitors with potential anti-malarial activity. However, this is a preliminary study of designing an inhibitor against Plasmodium falciparum 3D7; the results await justification by in vitro and in vivo experimentations.
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Affiliation(s)
- Md. Anayet Hasan
- />Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chittagong, 4331 Bangladesh
| | - Md. Habibul Hasan Mazumder
- />Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chittagong, 4331 Bangladesh
| | - Afrin Sultana Chowdhury
- />Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chittagong, 4331 Bangladesh
| | - Amit Datta
- />Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chittagong, 4331 Bangladesh
| | - Md. Arif Khan
- />Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail, 1902 Bangladesh
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