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Dwivedi M, Jose S, Gupta M, Devi SS, Raj R, Kumar D. Copper transporter protein (MctB) as a therapeutic target to elicit antimycobacterial activity against tuberculosis. J Biomol Struct Dyn 2024; 42:5334-5348. [PMID: 37340670 DOI: 10.1080/07391102.2023.2226728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 06/10/2023] [Indexed: 06/22/2023]
Abstract
Tuberculosis (TB) is a prehistoric infection and major etiologic agent of TB, Mycobacterium tuberculosis, which is considered to have advanced from an early progenitor species found in Eastern Africa. By the 1800s, there were approximately 800 to 1000 fatality case reports per 100,000 people in Europe and North America. This research suggests an In-silico study to identify potential inhibitory compounds for the target Mycobacterial copper transport protein (Mctb). ADME-based virtual screening, molecular docking, and molecular dynamics simulations were conducted to find promising compounds to modulate the function of the target protein. Four chemical compounds, namely Anti-MCT1, Anti-MCT2, Anti-MCT3 and Anti-MCT4 out of 1500 small molecules from the Diverse-lib of MTiOpenScreen were observed to completely satisfy Lipinski rule of five and Veber's rule. Further, significantly steady interactions with the MctB target protein were observed. Docking experiments have presented 9 compounds with less than -9.0 kcal/mol free binding energies and further MD simulation eventually gave 4 compounds having potential interactions and affinity with target protein and favorable binding energy ranging from -9.2 to -9.3 kcal/mol. We may propose these compounds as an effective candidate to reduce the growth of M. tuberculosis and may also assist present a novel therapeutic approach for Tuberculosis. In vivo and In vitro validation would be needed to proceed further in this direction.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Manish Dwivedi
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, India
| | - Sandra Jose
- Technology and Advanced Studies, Vels Institute of Science, Chennai, India
| | - Megha Gupta
- Vel Tech Rangarajan Dr Sagunthala R&D Institute of Science and Technology, Chennai, India
| | - Sreevidya S Devi
- Mar Athanasios College for Advanced Studies, Thiruvalla, Kerala, India
| | - Ritu Raj
- Centre of Biomedical Research (CBMR), SGPGIMS Campus, Lucknow, Uttar Pradesh, India
| | - Dinesh Kumar
- Centre of Biomedical Research (CBMR), SGPGIMS Campus, Lucknow, Uttar Pradesh, India
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2
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Borges EL, Goulart HA, Perin G, Schneider PH, Rieder GS, Nogara PA, da Rocha JBT. One-Pot Synthesis and in Silico Molecular Docking Studies of Arylselanyl Hydrazides as Potential Antituberculosis Agents. Chem Biodivers 2022; 19:e202100793. [PMID: 35293125 DOI: 10.1002/cbdv.202100793] [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: 10/01/2021] [Accepted: 03/14/2022] [Indexed: 11/06/2022]
Abstract
The present study reports a simple two-step method for the synthesis of arylselanyl hydrazide derivatives using hypophosphorous acid and polyethylene glycol (H3 PO2 /PEG-400) as an alternative reducing system and hydrazine hydrate (NH2 NH2 ⋅xH2 O/50-60 %). This single-vessel procedure was employed with methyl acrylate 2a and methyl bromoacetate 2b using diaryl diselenides to generate the nucleophile species to produce, respectively, 3-(arylselanyl)propane-hydrazides 4a-e and 2-(arylselanyl)acetohydrazides 5a-e with good yields by accelerating the reduction of -Se-Se- bond, when compared to available methods. The synthesized molecules are structurally similar to the isoniazid (INH). Therefore, we perform in silico molecular docking studies, using the lactoperoxidase enzyme, in order to verify whether the INH Se derivatives could interact in a similar way to INH at the active site of the mammalian enzyme. The in silico results indicated a similar type of interaction of the arylselanyl hydrazide derivatives with that of INH. In view of the similar in silico interaction of the selenium derivatives of INH, the arylselanyl hydrazide derivatives reported here should be tested against Mycobacterium tuberculosis in vitro.
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Affiliation(s)
- Elton L Borges
- Grupo de Pesquisa em Síntese Orgânica da Região Amazônica (LASORA, DAEPA), Fundação Universidade Federal de Rondônia (UNIR), Rua da Paz 4376, 76916-000, Presidente Médici, RO, Brazil
| | - Helen A Goulart
- Laboratório de Síntese Orgânica Limpa (LASOL, CCQFA), Universidade Federal de Pelotas (UFPel), PO Box 354, 96010-900, Pelotas, RS, Brazil
| | - Gelson Perin
- Laboratório de Síntese Orgânica Limpa (LASOL, CCQFA), Universidade Federal de Pelotas (UFPel), PO Box 354, 96010-900, Pelotas, RS, Brazil
| | - Paulo H Schneider
- Instituto de Química, Universidade Federal do Rio Grande do Sul (UFRGS), 91501-970, Porto Alegre, RS, Brazil
| | - Guilherme S Rieder
- Programa de Pós-graduação em Ciências Biológicas: Bioquímica Toxicológica, Universidade Federal de Santa Maria (UFSM), 97105-90, Santa Maria, RS, Brazil
| | - Pablo A Nogara
- Programa de Pós-graduação em Ciências Biológicas: Bioquímica Toxicológica, Universidade Federal de Santa Maria (UFSM), 97105-90, Santa Maria, RS, Brazil
| | - João B T da Rocha
- Programa de Pós-graduação em Ciências Biológicas: Bioquímica Toxicológica, Universidade Federal de Santa Maria (UFSM), 97105-90, Santa Maria, RS, Brazil
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3
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Xu Y, Liu S, Bian L, Li Z, Luo C, Chen Y, Wu X. Engineering of a UDP-Glycosyltransferase for the Efficient Whole-Cell Biosynthesis of Siamenoside I in Escherichia coli. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:1601-1609. [PMID: 35099964 DOI: 10.1021/acs.jafc.1c07699] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The combination of the insufficient availability and the complex structure of siamenoside I (SI), the sweetest glucoside isolated from Siraitia grosvenorii to date, limited its use as a natural sweetener. To solve this problem, an improved biocatalyst, UGT-M2, was semi-rationally created by engineering the uridine diphosphate glycosyltransferase UGT94-289-2 from S. grosvenorii for the monoglucosylation of mogroside IIIE (MG IIIE) to SI. Subsequently, an engineered Escherichia coli cell was constructed, which combined UGT-M2 with a UDP-glucose regeneration system to circumvent the need for expensive UDP-glucose to produce SI. After optimization, high-purity SI (>96.4%) was efficiently prepared from MG IIIE at a 1 L scale with a productivity of 29.78 g/(L day) and a molar yield of 76.5% and without using exogenous UDP-glucose. This study not only developed a whole-cell approach for the preparation of SI but also provided an alternative glycosyltransferase variant for SI biosynthesis with synthetic biology in the future.
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Affiliation(s)
- Yuncong Xu
- Department of Biochemistry, College of Life Sciences and Technology, China Pharmaceutical University, 639 Longmian Road, Nanjing, Jiangsu Province 211198, PR China
| | - Shiqiang Liu
- Department of Biochemistry, College of Life Sciences and Technology, China Pharmaceutical University, 639 Longmian Road, Nanjing, Jiangsu Province 211198, PR China
| | - Liuyun Bian
- Department of Biochemistry, College of Life Sciences and Technology, China Pharmaceutical University, 639 Longmian Road, Nanjing, Jiangsu Province 211198, PR China
| | - Zhenlin Li
- Department of Pharmaceutical Analysis and Metabolomics, Jiangsu Province Academy of Traditional Chinese Medicine, 100 Shizi Street. Hongshan Road, Nanjing, Jiangsu Province 210028, PR China
| | - Chen Luo
- Department of Biochemistry, College of Life Sciences and Technology, China Pharmaceutical University, 639 Longmian Road, Nanjing, Jiangsu Province 211198, PR China
| | - Yijun Chen
- Laboratory of Chemical Biology, College of Life Sciences and Technology, China Pharmaceutical University, 639 Longmian Road, Nanjing, Jiangsu Province 211198, PR China
| | - Xuri Wu
- Department of Biochemistry, College of Life Sciences and Technology, China Pharmaceutical University, 639 Longmian Road, Nanjing, Jiangsu Province 211198, PR China
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4
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Muthumanickam S, Kamaladevi A, Boomi P, Gowrishankar S, Pandian SK. Indian Ethnomedicinal Phytochemicals as Promising Inhibitors of RNA-Binding Domain of SARS-CoV-2 Nucleocapsid Phosphoprotein: An In Silico Study. Front Mol Biosci 2021; 8:637329. [PMID: 34277698 PMCID: PMC8283196 DOI: 10.3389/fmolb.2021.637329] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 02/11/2021] [Indexed: 11/16/2022] Open
Abstract
SARS-CoV-2, an etiological agent of COVID-19, has been the reason for the unexpected global pandemic, causing severe mortality and imposing devastative effects on public health. Despite extensive research work put forward by scientist around globe, so far, no suitable drug or vaccine (safe, affordable, and efficacious) has been identified to treat SARS-CoV-2. As an alternative way of improvising the COVID-19 treatment strategy, that is, strengthening of host immune system, a great deal of attention has been given to phytocompounds from medicinal herbs worldwide. In a similar fashion, the present study deliberately focuses on the phytochemicals of three Indian herbal medicinal plants viz., Mentha arvensis, Coriandrum sativum, and Ocimum sanctum for their efficacy to target well-recognized viral receptor protein through molecular docking and dynamic analyses. Nucleocapsid phosphoprotein (N) of SARS-CoV-2, being a pivotal player in replication, transcription, and viral genome assembly, has been recognized as one of the most attractive viral receptor protein targets for controlling the viral multiplication in the host. Out of 127 phytochemicals screened, nine (linarin, eudesmol, cadinene, geranyl acetate, alpha-thujene, germacrene A, kaempferol-3-O-glucuronide, kaempferide, and baicalin) were found to be phenomenal in terms of exhibiting high binding affinity toward the catalytic pocket of target N-protein. Further, the ADMET prediction analysis unveiled the non-tumorigenic, noncarcinogenic, nontoxic, non-mutagenic, and nonreproductive nature of the identified bioactive molecules. Furthermore, the data of molecular dynamic simulation validated the conformational and dynamic stability of the docked complexes. Concomitantly, the data of the present study validated the anti-COVID efficacy of the bioactives from selected medicinal plants of Indian origin.
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Affiliation(s)
| | - Arumugam Kamaladevi
- Department of Animal Science, School of Life Sciences, Bharathidasan University, Tiruchirappalli, India
| | - Pandi Boomi
- Department of Bioinformatics, Alagappa University, Karaikudi, India
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Zhang Z, Han Q, Mao X, Liu J, Wang W, Li D, Zhou F, Ke Y, Xu L, Hu L. Discovery of novel SecA inhibitors against "Candidatus Liberibacter asiaticus" through virtual screening and biological evaluation. Chem Biol Drug Des 2021; 98:395-404. [PMID: 33963664 DOI: 10.1111/cbdd.13859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 02/07/2021] [Accepted: 03/14/2021] [Indexed: 11/26/2022]
Abstract
"Candidatus Liberibacter asiaticus" (Ca. L. asiaticus) is the causal agent of Huanglongbing disease of citrus and current study focuses on the discovery of novel small-molecule inhibitors against SecA protein of Ca. L. asiaticus. In this study, homologous modeling was used to construct the three-dimensional structure of SecA. Then, molecular docking-based virtual screening and two rounds of in vitro bacteriostatic experiments were utilized to identify novel small-molecule inhibitors of SecA. Encouragingly, 93 compounds were obtained and two of them (P684-2850, P684-3808) showed strong antimicrobial activities against Liberibacter crescens BT-1 in bacteriostatic experiments. Finally, molecular dynamics simulations were employed to explore the binding modes of the receptor-ligand complexes. Results in MD simulations showed that compound P684-3808 was relatively stable during simulation, while compound P684-2850 left the binding pocket. Compound P684-3808 might be suitable as a lead compound for further development of antimicrobial compounds against SecA of Ca. L. asiaticus.
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Affiliation(s)
- Zhengfang Zhang
- Zhejiang Yangshengtang Institute of Natural Medication Co., Ltd, Hangzhou, China
| | - Quan Han
- Zhejiang Yangshengtang Institute of Natural Medication Co., Ltd, Hangzhou, China
| | - Xiongxing Mao
- Zhejiang Yangshengtang Institute of Natural Medication Co., Ltd, Hangzhou, China
| | - Jinhua Liu
- Zhejiang Yangshengtang Institute of Natural Medication Co., Ltd, Hangzhou, China
| | - Wei Wang
- Zhejiang Yangshengtang Institute of Natural Medication Co., Ltd, Hangzhou, China
| | - Dong Li
- Zhejiang Yangshengtang Institute of Natural Medication Co., Ltd, Hangzhou, China
| | - Feng Zhou
- Zhejiang Yangshengtang Institute of Natural Medication Co., Ltd, Hangzhou, China
| | - Yang Ke
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Lei Xu
- Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou, China
| | - Liu Hu
- Zhejiang Yangshengtang Institute of Natural Medication Co., Ltd, Hangzhou, China
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6
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Li P, Tian J, Guo C, Luo S, Li J. Interaction of gibberellin and other hormones in almond anthers: phenotypic and physiological changes and transcriptomic reprogramming. HORTICULTURE RESEARCH 2021; 8:94. [PMID: 33931608 PMCID: PMC8087710 DOI: 10.1038/s41438-021-00527-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 01/23/2021] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
Low temperature causes anther dysfunction, severe pollen sterility and, ultimately, major yield losses in crop plants. Previous studies have shown that the gibberellic acid (GA) metabolic pathway plays an important role in this process by regulating tapetum function and pollen development. However, the interaction mechanism of GA with other hormones mediating anther development is still unclear. Herein, we collected and analyzed almond (Amygdalus communis L.) anthers at the meiosis, tetrad, 1-nucleus, and mature 2-nucleus stages. The growth rate per 1000 anthers exhibited a significant positive correlation with the total bioactive GA compound content, and the levels of all bioactive GA compounds were highest in the 1-nucleus pollen stage. GA3 treatment experiments indicated that exogenous GA3 increased the levels of indole-3-acetic acid (IAA), trans-zeatin (tZ), and jasmonic acid (JA) and decreased the levels of salicylic acid (SA) and abscisic acid (ABA); moreover, GA3 improved pollen viability and quantities under cold conditions, whereas PP333 (paclobutrazol, an inhibitor of GA biosynthesis) was antagonistic with GA3 in controlling anther development. RNA-seq and qRT-PCR results showed that GA played an important role in anther development by regulating the expression of other phytohormone pathway genes, dehydration-responsive element-binding/C-repeat binding factor (DREB1/CBF)-mediated signaling genes, and anther development pathway genes. Our results reveal the novel finding that GA interacts with other hormones to balance anther development under normal- and low-temperature conditions in almond.
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Affiliation(s)
- Peng Li
- College of Forestry and Horticulture, Xinjiang Agricultural University, Urumqi, 830052, China
- Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, 125100, China
| | - Jia Tian
- College of Forestry and Horticulture, Xinjiang Agricultural University, Urumqi, 830052, China
| | - Changkui Guo
- School of Agriculture and Food Science, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, China.
| | - Shuping Luo
- College of Forestry and Horticulture, Xinjiang Agricultural University, Urumqi, 830052, China
| | - Jiang Li
- College of Forestry and Horticulture, Xinjiang Agricultural University, Urumqi, 830052, China.
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7
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Gu X, Wang Y, Wang H, Wu H, Li W, Wang J, Li N. Homology modeling, molecular dynamics and virtual screening of endothelin-A receptor for the treatment of pulmonary arterial hypertension. J Biomol Struct Dyn 2020; 39:3912-3923. [PMID: 32431219 DOI: 10.1080/07391102.2020.1772106] [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: 10/24/2022]
Abstract
Pulmonary arterial hypertension (PAH) is a progressive disease of pulmonary arteries, causing serious shortness of breath and right ventricular failure with high mortality. Numerous studies have verified that the symptoms of PAH could be attenuated effectively with endothelin-A receptor (ETAR) antagonists. Unfortunately, the 3D structure of ETAR has not been released, making it difficult to understand the interactions between ETAR and its antagonists. In this study, computational methods including homology modeling, molecular docking and molecular dynamics simulations were performed to build the structure of ETAR and predict the binding patterns of ETAR with its two antagonists. Based on these results, virtual screening study was implemented against Traditional Chinese Medicine (TCM) database to identify novel natural ETAR antagonists. Six compounds with best binding energies were screened out and two of them were found to bind steadily with ETAR validated through molecular dynamics simulations and MM-GBSA calculation, indicating that they were potential antagonists of ETAR. In a word, our research provided a deep exploration into the interaction between ETAR and its antagonists, which could promote the development of novel therapy against PAH.[Formula: see text]Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Xi Gu
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, P. R. China.,Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, P. R. China
| | - Ying Wang
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, P. R. China.,Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, P. R. China
| | - Hanxun Wang
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, P. R. China.,School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, P. R. China
| | - Hairui Wu
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, P. R. China.,School of Life Sciences and Biopharmaceutical Science, Shenyang Pharmaceutical University, Shenyang, P.R. China
| | - Wei Li
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, P. R. China.,School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, P. R. China
| | - Jian Wang
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, P. R. China.,School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, P. R. China
| | - Ning Li
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, P. R. China.,Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, P. R. China
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8
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Ligand-based virtual screening, consensus molecular docking, multi-target analysis and comprehensive ADMET profiling and MD stimulation to find out noteworthy tyrosine kinase inhibitor with better efficacy and accuracy. ADVANCES IN TRADITIONAL MEDICINE 2019. [DOI: 10.1007/s13596-019-00406-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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9
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Pharmacoinformatics-based identification of anti-bacterial catalase-peroxidase enzyme inhibitors. Comput Biol Chem 2019; 83:107136. [DOI: 10.1016/j.compbiolchem.2019.107136] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 09/28/2019] [Accepted: 09/29/2019] [Indexed: 11/17/2022]
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10
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Raka SC, Ahamed R, Rahman A, Momen AZMR. In silico discovery of noteworthy multi-targeted acetylcholinesterase inhibitors for the treatment of Alzheimer’s disease. ADVANCES IN TRADITIONAL MEDICINE 2019. [DOI: 10.1007/s13596-019-00407-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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11
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Lanka G, Bathula R, Dasari M, Nakkala S, Bhargavi M, Somadi G, Potlapally SR. Structure-based identification of potential novel inhibitors targeting FAM3B (PANDER) causing type 2 diabetes mellitus through virtual screening. J Recept Signal Transduct Res 2019; 39:253-263. [PMID: 31517548 DOI: 10.1080/10799893.2019.1660897] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Type 2 diabetes mellitus is a metabolic disorder that requires potent therapeutic approaches. The FAM3B is a cytokine-like protein also referred to as PANcreatic-DERrived factor (PANDER) which mainly exists in pancreatic islets. In the process of identifying potential inhibitors with the aid of structure-based method PANDER protein is identified as a novel therapeutic target against type 2 diabetes mellitus as it involved in the development of type 2 diabetes by negatively regulating the pancreatic β-cell function and insulin sensitivity in the liver. In the present study, the 3d model of target protein FAM3B was generated by homology modeling technique using the MODELLER9.9 program. The assessment of the structural stability of the 3d model was established by energy minimization technique. The structural quality was evaluated with standard validating protocols. Binding regions of the target protein has been determined by literature and SiteMap tool. In the current study of research, the FAM3B model was subjected to molecular screening with the Asinex-elite database of 14849 output molecules using the Glide virtual screening module in the Schrodinger suite. The final XP descriptor output of 14 molecules was analyzed and prioritized based on molecular interactions at the FAM3B active site. The docking score, binding free energies (Prime MM/GBSA) and bioavailability were undertaken into the consideration to identify lead inhibitors. The identified lead compounds were checked for ADME properties all falling within the permeable ranges. The analysis of results gave the insight to develop the novel therapeutic strategies against type 2 diabetes mellitus.
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Affiliation(s)
- Goverdhan Lanka
- Molecular Modeling Laboratory, Department of Chemistry, Nizam College, Osmania University , Basheerbagh , Hyderabad , India
| | - Revanth Bathula
- Molecular Modeling Laboratory, Department of Chemistry, Nizam College, Osmania University , Basheerbagh , Hyderabad , India
| | - Mahendar Dasari
- Molecular Modeling Laboratory, Department of Chemistry, Nizam College, Osmania University , Basheerbagh , Hyderabad , India
| | - Sravanthi Nakkala
- Molecular Modeling Laboratory, Department of Chemistry, Nizam College, Osmania University , Basheerbagh , Hyderabad , India
| | - Manan Bhargavi
- Molecular Modeling Laboratory, Department of Chemistry, Nizam College, Osmania University , Basheerbagh , Hyderabad , India
| | - Gururaj Somadi
- Molecular Modeling Laboratory, Department of Chemistry, Nizam College, Osmania University , Basheerbagh , Hyderabad , India
| | - Sarita Rajender Potlapally
- Molecular Modeling Laboratory, Department of Chemistry, Nizam College, Osmania University , Basheerbagh , Hyderabad , India
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12
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Liu X, Li W, Hu B, Wang M, Wang J, Guan L. Identification of isobavachalcone as a potential drug for rice blast disease caused by the fungus Magnaporthe grisea. J Biomol Struct Dyn 2018; 37:3399-3409. [PMID: 30132740 DOI: 10.1080/07391102.2018.1515117] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The rice blast disease caused by the fungus Magnaporthe grisea is one of the most devastating rice diseases, but there is no effective fungicide toward chitinase which is a key enzyme of M. grisea. In this study, we observed that distortion and cell-wall damage of M. grisea hyphae were significantly under the scanning electron micrograph after a 24-h treatment with 10 mg/L isobavachalcone (IBC) extracted from Psoralea corylifolia L. To further explore the effect of IBC on the cell wall of M. grisea, we examined changes in enzymes associated with cell wall degradation by enzyme activity experiments, treated liquid culture mycelia with 10 mg/L IBC for 1 h. Results displayed that chitinase was obviously more active than control group. To illustrate the interactions between IBC and chitinase, the studies of homology modeling and molecular docking were carried out successively. The results revealed that IBC had hydrogen bonds with residues ASP267 and ARG276 of chitinase. Besides, these nonpolar residues TYR270, PRO271, VAL272, LEU310, PRO311, TYR316, and LEU317 were able to form strong hydrophobic interactions. Binding energies of the chitinase-IBC complexes were calculated by MM-GBSA showed that the ΔGbind score of molecular dynamics had lower binding energy and more stable than docking complexes. All above, IBC owns significant agonistic activity in chitinase and would be a potent fungicide to inhibit the growth of M. grisea. We hope the above information provides an important insight for understanding the interactions between IBC and chitinase, which may be useful in the discovery of a novel potent agonist. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Xue Liu
- a Department of Pharmaceutical and Biological Engineering , Shenyang University of Chemical Technology , Shenyang , China
| | - Wei Li
- a Department of Pharmaceutical and Biological Engineering , Shenyang University of Chemical Technology , Shenyang , China
| | - Baichun Hu
- b Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education , Shenyang Pharmaceutical University , Shenyang , China
| | - Mingxing Wang
- b Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education , Shenyang Pharmaceutical University , Shenyang , China
| | - Jian Wang
- b Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education , Shenyang Pharmaceutical University , Shenyang , China
| | - Lijie Guan
- a Department of Pharmaceutical and Biological Engineering , Shenyang University of Chemical Technology , Shenyang , China
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13
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Liu Q, Li L, Xu F. Systematic analysis and integrative discovery of active-site subpocket-specific dehydroquinate synthase inhibitors combating antibiotic-resistant Staphylococcus aureus infection. J Bioinform Comput Biol 2018; 16:1850027. [PMID: 30567475 DOI: 10.1142/s0219720018500270] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Shikimate pathway plays an essential role in the biosynthesis of aromatic amino acids in various plants and bacteria, which consists of seven key enzymes and they are all attractive targets for antibacterial agent development due to their absence in humans. The Staphylococcus aureus dehydroquinate synthase (SaDHQS) is involved in the second step of shikimate pathway, which catalyzes the NAD <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msup><mml:mrow/><mml:mrow><mml:mo>+</mml:mo></mml:mrow></mml:msup></mml:math> -dependent conversion of 3-deoxy-D-arabino-heptulosonate-7-phosphate to dehydroquinate via multiple steps. The enzyme active site can be characterized by two spatially separated subpockets 1 and 2, which represent the reaction center of substrate adduct with NAD <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msup><mml:mrow/><mml:mrow><mml:mo>+</mml:mo></mml:mrow></mml:msup></mml:math> nicotinamide moiety and the assistant binding site of NAD <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msup><mml:mrow/><mml:mrow><mml:mo>+</mml:mo></mml:mrow></mml:msup></mml:math> adenine moiety, respectively. In silico virtual screening is performed against a biogenic compound library to discover SaDHQS subpocket-specific inhibitors, which were then tested against both antibiotic-sensitive and antibiotic-resistant S. aureus strains by using in vitro susceptibility test. The activity profile of hit compounds has no considerable difference between the antibiotic-sensitive and -resistant strains. The subpocket 1-specific inhibitors exhibit a generally higher activity than subpocket 2-specific inhibitors, and they also hold a strong selectivity between their cognate and noncognate subpockets. Dynamics and energetics analyses reveal that the SaDHQS active site prefers to interact with amphipathic and polar inhibitors by forming multiple hydrogen bonds and van der Waals packing at the complex interfaces of the two subpockets with their cognate inhibitors.
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Affiliation(s)
- Quanfeng Liu
- Department of Anesthesiology, Yidu Central Hospital Affiliated to Weifang Medical University, Qingzhou 262500, P. R. China
| | - Liping Li
- Department of Obstetrics, Yidu Central Hospital Affiliated to Weifang Medical University, Qingzhou 262500, P. R. China
| | - Fei Xu
- Department of Anesthesiology, Yidu Central Hospital Affiliated to Weifang Medical University, Qingzhou 262500, P. R. China
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Wang K, Zhu M, Tang Y, Liu J, Yan F, Yu Z, Zhu J. Integration of virtual screening and susceptibility test to discover active-site subpocket-specific biogenic inhibitors of Helicobacter pylori shikimate dehydrogenase. Int Microbiol 2018; 22:69-80. [PMID: 30810934 DOI: 10.1007/s10123-018-0029-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 07/24/2018] [Accepted: 08/06/2018] [Indexed: 12/25/2022]
Abstract
Shikimate dehydrogenase (HpSDH) (EC 1.1.1.25) is a key enzyme in the shikimate pathway of Helicobacter pylori (H. pylori), which catalyzes the NADPH-dependent reversible reduction of 3-dehydroshikimate to shikimate. Targeting HpSDH has been recognized as an attractive therapeutic strategy against H. pylori infection. Here, the catalytic active site in the crystal structure of HpSDH in complex with its substrate NADPH and product shikimate was examined in detail; the site can be divided into three spatially separated subpockets that separately correspond to the binding regions of shikimate, NADPH dihydronicotinamide moiety, and NADPH adenine moiety. Subsequently, a cascading protocol that integrated virtual screening and antibacterial test was performed against a biogenic compound library to identify biologically active, subpocket-specific inhibitors. Consequently, five, eight, and six promising compounds for, respectively, subpockets 1, 2, and 3 were selected from the top-100 docking-ranked hits, from which 11 compounds were determined to have high or moderate antibacterial potencies against two reference H. pylori strains, with MIC range between 8 and 93 μg/mL. It is found that the HpSDH active site prefers to accommodate amphipathic and polar inhibitors that consist of an aromatic core as well as a number of oxygen-rich polar/charged substituents such as hydroxyl, carbonyl, and carboxyl groups. Subpockets 1- and 2-specific inhibitors exhibit a generally higher activity than subpocket 3-specific inhibitors. Molecular dynamics simulations revealed an intense nonbonded network of hydrogen bonds, π-π stacking, and van der Waals contacts at the tightly packed complex interfaces of active-site subpockets with their cognate inhibitors, conferring strong stability and specificity to these complex systems. Binding energetic analysis demonstrated that the identified potent inhibitors can target their cognate subpockets with an effective selectivity over noncognate ones.
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Affiliation(s)
- Kuifeng Wang
- Department of Infectious Diseases, Affiliated Taizhou Hospital of Wenzhou Medical University, No.50 Ximeng Road, Taizhou, 317000, China
| | - Min Zhu
- Department of Infectious Diseases, Affiliated Taizhou Hospital of Wenzhou Medical University, No.50 Ximeng Road, Taizhou, 317000, China
| | - Yongzhi Tang
- Department of Infectious Diseases, Affiliated Taizhou Hospital of Wenzhou Medical University, No.50 Ximeng Road, Taizhou, 317000, China
| | - Junyan Liu
- Department of Infectious Diseases, Affiliated Taizhou Hospital of Wenzhou Medical University, No.50 Ximeng Road, Taizhou, 317000, China
| | - Fei Yan
- Department of Infectious Diseases, Affiliated Taizhou Hospital of Wenzhou Medical University, No.50 Ximeng Road, Taizhou, 317000, China
| | - Zhenjun Yu
- Department of Infectious Diseases, Affiliated Taizhou Hospital of Wenzhou Medical University, No.50 Ximeng Road, Taizhou, 317000, China
| | - Jiansheng Zhu
- Department of Infectious Diseases, Affiliated Taizhou Hospital of Wenzhou Medical University, No.50 Ximeng Road, Taizhou, 317000, China.
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Recent advances in metabolic engineering of Corynebacterium glutamicum for bioproduction of value-added aromatic chemicals and natural products. Appl Microbiol Biotechnol 2018; 102:8685-8705. [DOI: 10.1007/s00253-018-9289-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 07/30/2018] [Accepted: 07/31/2018] [Indexed: 02/06/2023]
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