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Mubarak SJ, Gupta S, Vedagiri H. Scaffold Hopping and Screening for Potent Small Molecule Agonists for GRP94: Implications to Alleviate ER Stress-Associated Pathogenesis. Mol Biotechnol 2024; 66:737-755. [PMID: 36763304 DOI: 10.1007/s12033-023-00685-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 01/27/2023] [Indexed: 02/11/2023]
Abstract
Disparity in the activity of Endoplasmic reticulum (ER) leads to degenerative diseases, mainly associated with protein misfolding and aggregation leading to cellular dysfunction and damage, ultimately contributing to ER stress. ER stress activates the complex network of Unfolded Protein Response (UPR) signaling pathways mediated by transmembrane proteins IRE1, ATF6, and PERK. In addition to UPR, many ER chaperones have evolved to optimize the output of properly folded secretory and membrane proteins. Glucose-regulated protein 94 (GRP94), an ER chaperone of heat shock protein HSP90 family, directs protein folding through interaction with other components of the ER protein folding machinery and assists in ER-associated degradation (ERAD). Activation of GRP94 would increase the efficacy of protein folding machinery and regulate the UPR pathway toward homeostasis. The present study aims to screen for novel agonists for GRP94 based on Core hopping, pharmacophore hypothesis, 3D-QSAR, and virtual screening with small-molecule compound libraries in order to improve the efficiency of native protein folding by enhancing GRP94 chaperone activity, therefore to reduce protein misfolding and aggregation. In this study, we have employed the strategy of small molecule-dependent ER programming to enhance the chaperone activity of GRP94 through scaffold hopping-based screening approach to identify specific GRP94 agonists. New scaffolds generated by altering the cores of NECA, the known GRP94 agonist, were validated by employing pharmacophore hypothesis testing, 3D-QSAR modeling, and molecular dynamics simulations. This facilitated the identification of small molecules to improve the efficiency of native protein folding by enhancing GRP94 activity. High-throughput virtual screening of the selected pharmacophore hypothesis against Selleckchem and ZINC databases retrieved a total of 2,27,081 compounds. Further analysis on docking and ADMET properties revealed Epimedin A, Narcissoside, Eriocitrin 1,2,3,4,6-O-Pentagalloylglucose, Secoisolariciresinol diglucoside, ZINC92952357, ZINC67650204, and ZINC72457930 as potential lead molecules. The stability and interaction of these small molecules were far better than the known agonist, NECA indicating their efficacy in selectively alleviating ER stress-associated pathogenesis. These results substantiate the fact that small molecule-dependent ER reprogramming would activate the ER chaperones and therefore reduce the protein misfolding as well as aggregation associated with ER stress in order to restore cellular homeostasis.
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Affiliation(s)
| | - Surabhi Gupta
- Department of Reproductive Biology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Hemamalini Vedagiri
- Department of Bioinformatics, Bharathiar University, Coimbatore, Tamil Nadu, India.
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Behera DU, Gaur M, Sahoo M, Subudhi E, Subudhi BB. Development of pharmacophore models for AcrB protein and the identification of potential adjuvant candidates for overcoming efflux-mediated colistin resistance. RSC Med Chem 2024; 15:127-138. [PMID: 38283226 PMCID: PMC10809322 DOI: 10.1039/d3md00483j] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 10/26/2023] [Indexed: 01/30/2024] Open
Abstract
Growing multi-drug resistance (MDR) among ESKAPE pathogens is a huge challenge. Increased resistance to last-resort antibiotics, like colistin, has further aggravated this. Efflux is identified as a major route of colistin resistance. So, finding an FDA-approved efflux inhibitor for potential application as an adjuvant to colistin was the primary objective of this study. E. coli-AcrB pump inhibitors and substrates were used to develop and validate the pharmacophoric model. Drugs confirming this pharmacophore were subjected to molecular docking to identify hits for the AcrB binding pocket. The efflux inhibition potential of the top hit was validated through the in vitro evaluation of the minimum inhibitory concentration (MIC) in combination with colistin. The checkerboard assay was done to demonstrate synergism, which was further corroborated by the Time-kill assay. Ten common pharmacophore hypotheses were successfully generated using substrate/inhibitors. Following enrichment analysis, AHHNR.100 was identified as the top-ranked hypothesis, and 207 unique compounds were found to conform to this hypothesis. The multi-step docking of these compounds against the AcrB protein revealed argatroban as the top non-antibiotic hit. This significantly inhibited the efflux activity of colistin-resistant clinical isolates K. pneumoniae (n = 1) and M. morganii (n = 2). Further, their combination with colistin enhanced the susceptibility of these isolates, and the effect was found to be synergistic. Accordingly, the time-kill assay of this combination showed 8-log and 2-log reductions against K. pneumoniae and M. morganii, respectively. In conclusion, this study found argatroban as a bacterial efflux inhibitor that can be potentially used to overcome efflux-mediated resistance.
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Affiliation(s)
- Dibyajyoti Uttameswar Behera
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University) Kalinga Nagar, Ghatikia Bhubaneswar-751003 Odisha India +91 9861075829
| | - Mahendra Gaur
- Drug Development and Analysis Laboratory, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University) Kalinga Nagar, Ghatikia Bhubaneswar-751003 Odisha India +91 7978085389
- Department of Biotechnology & Food Technology, Punjabi University Patiala 147002 India
| | - Maheswata Sahoo
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University) Kalinga Nagar, Ghatikia Bhubaneswar-751003 Odisha India +91 9861075829
| | - Enketeswara Subudhi
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University) Kalinga Nagar, Ghatikia Bhubaneswar-751003 Odisha India +91 9861075829
| | - Bharat Bhusan Subudhi
- Drug Development and Analysis Laboratory, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University) Kalinga Nagar, Ghatikia Bhubaneswar-751003 Odisha India +91 7978085389
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Zhang J, Tu Z, Wen P, Wang H, Hu Y. Peptidomics Screening and Molecular Docking with Umami Receptors T1R1/T1R3 of Novel Umami Peptides from Oyster ( Crassostrea gigas) Hydrolysates. J Agric Food Chem 2024; 72:634-646. [PMID: 38131198 DOI: 10.1021/acs.jafc.3c06859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
In this study, novel umami peptides were prepared from oyster (Crassostrea gigas) hydrolysates, and their umami mechanisms were investigated. Umami fractions G2 and G3 were isolated by gel filtration chromatography (GFC) and sensory evaluation. The umami scores of the G2 and G3 fractions were 7.8 ± 0.12 and 7.5 ± 0.18, respectively. 36 potential umami peptides with molecular weights below 1500 Da, E and D accounting for >30% of the peptides and iUmami-SCM > 588 were screened by peptidomics. Peptide source analysis revealed that myosin, paramyosin, and sarcoplasmic were the major precursor proteins for these peptides. The electronic tongue results demonstrated that the synthetic peptides DPNDPDMKY and NARIEELEEE possessed an umami characteristic, whereas SIEDVEESRNK and ISIEDVEESRNK possessed a saltiness characteristic. Additionally, molecular docking results indicated that the umami peptide (DPNDPDMKY, NARIEELEEE, SIEDVEESRNK, and ISIEDVEESRNK) binds to H145, S276, H388, T305, Y218, D216, and Q389 residues in the T1R3 taste receptor via a conventional hydrogen bond and a carbon-hydrogen bond. This research provides a new strategy for the screening of umami peptides.
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Affiliation(s)
- Junwei Zhang
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, Jiangxi 330047, China
- Jiangxi Normal University (Qinzhou) Research Centre for High Value Comprehensive Utilization of Agricultural Products, Qinzhou, Guangxi 535000, China
| | - Zongcai Tu
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, Jiangxi 330047, China
- National R&D Center of Freshwater Fish Processing and Engineering Research Center of Freshwater Fish High-Value Utilization of Jiangxi Province, Jiangxi Normal University, Nanchang, Jiangxi 330022, China
| | - Pingwei Wen
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, Jiangxi 330047, China
| | - Hui Wang
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, Jiangxi 330047, China
- Jiangxi Normal University (Qinzhou) Research Centre for High Value Comprehensive Utilization of Agricultural Products, Qinzhou, Guangxi 535000, China
| | - Yueming Hu
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, Jiangxi 330047, China
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Ren H, Zhou J, Fu H, Feng Q, Wang J, Li C, Xia G, Shang W, He Y. Identification and virtual screening of novel salty peptides from hydrolysate of tilapia by-product by batch molecular docking. Front Nutr 2024; 10:1343209. [PMID: 38260067 PMCID: PMC10800615 DOI: 10.3389/fnut.2023.1343209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 12/19/2023] [Indexed: 01/24/2024] Open
Abstract
Introduction Tilapia produces a large number of by-products during processing, which contain potentially flavorful peptides. Methods The application of PyRx software enabled batch molecular docking andscreening of 16 potential salty peptides from 189 peptides identified in the enzymaticdigestion of tilapia by-products. Results According to sensory analysis, all 16 peptides werepredominantly salty with a threshold of 0.256 - 0.379 mmol/L with some sournessand astringency, among which HLDDALR had the highest salty intensity, followedby VIEPLDIGDDKVR, FPGIPDHL, and DFKSPDDPSRH. I addition, moleculardocking results showed these four core peptides with high salt intensity bound to thesalt receptor TRPV1 mainly via van der Waals interactions, hydrogen bonds, andhydrophobic forces; Arg491, Tyr487, VAL441, and Asp708 were the key sites for thebinding of salty peptides to TRPV1. Therefore, the application of batch moleculardocking using PyRx is effective and economical for the virtual screening of saltypeptides.
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Affiliation(s)
- Hongjun Ren
- College of Food Science and Engineering, Hainan University, Haikou, China
| | - Jingxuan Zhou
- College of Food Science and Engineering, Hainan University, Haikou, China
| | - Huixian Fu
- College of Food Science and Engineering, Hainan University, Haikou, China
| | - Qiaohui Feng
- College of Food Science and Engineering, Hainan University, Haikou, China
| | - Jionghao Wang
- College of Food Science and Engineering, Hainan University, Haikou, China
| | - Chuan Li
- College of Food Science and Engineering, Hainan University, Haikou, China
- Hainan Provincial Engineering Research Centre of Aquatic Resources Efficient Utilization in the South China Sea, Haikou, China
- Key Laboratory of Seafood Processing of Haikou, Haikou, China
| | - Guanghua Xia
- College of Food Science and Engineering, Hainan University, Haikou, China
- Hainan Provincial Engineering Research Centre of Aquatic Resources Efficient Utilization in the South China Sea, Haikou, China
- Key Laboratory of Seafood Processing of Haikou, Haikou, China
| | - Wenting Shang
- College of Food Science and Engineering, Hainan University, Haikou, China
| | - Yanfu He
- College of Food Science and Engineering, Hainan University, Haikou, China
- Hainan Provincial Engineering Research Centre of Aquatic Resources Efficient Utilization in the South China Sea, Haikou, China
- Key Laboratory of Seafood Processing of Haikou, Haikou, China
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Jia R, Yang Y, Liao G, Gu D, Pu Y, Huang M, Wang G. Excavation, identification and structure-activity relationship of heat-stable umami peptides in the processing of Wuding chicken. Food Chem 2024; 430:137051. [PMID: 37541042 DOI: 10.1016/j.foodchem.2023.137051] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/27/2023] [Accepted: 07/27/2023] [Indexed: 08/06/2023]
Abstract
Umami peptides from different stages of Wuding chicken processing were discovered, isolated, and purified using ultrafiltration membrane, gel filtration chromatography, and reversed-phase high-performance liquid chromatography, and the binding mechanism was explored. Twelve umami peptides were found by nano-scale liquid chromatography-tandem mass spectrometry, three of which (HLEEEIK, LDDALR, and ELY) existed throughout the processing step. The umami score and the frequency of active fragments of umami were highest for LEEEL, followed by EEF. The main active sites between umami peptide and receptor T1R1/T1R3 were Tyr262, Glu325, and Glu292, and hydrophobic interaction and hydrogen bonding were the main forces, and bitter amino acids were also important components of umami peptides. It was found for the first time that heat-stable umami peptides exist in Wuding chickens, which provides a basis for the identification and screening of umami peptides in local chickens, and also helps to study the structure-activity relationship of umami peptides.
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Affiliation(s)
- Rong Jia
- College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, China; Livestock Product Processing and Engineering Technology Research Center of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
| | - Yuan Yang
- College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, China; Livestock Product Processing and Engineering Technology Research Center of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
| | - Guozhou Liao
- Livestock Product Processing and Engineering Technology Research Center of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China.
| | - Dahai Gu
- College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, China; Livestock Product Processing and Engineering Technology Research Center of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
| | - Yuehong Pu
- College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, China; Livestock Product Processing and Engineering Technology Research Center of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
| | - Ming Huang
- Key Laboratory of Meat Processing and Quality Control, MOE, Key Laboratory of Meat Processing, MOA, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Guiying Wang
- College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, China; Livestock Product Processing and Engineering Technology Research Center of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China.
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Abd El-Aziz NM, Moharam ME, El-Gamal NN, Khalil BE. Enhancement of novel Endo-polygalacturonase expression in Rhodotorula mucilaginosa PY18: insights from mutagenesis and molecular docking. Microb Cell Fact 2023; 22:252. [PMID: 38066588 PMCID: PMC10709964 DOI: 10.1186/s12934-023-02253-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 11/16/2023] [Indexed: 12/18/2023] Open
Abstract
Pectinase is a particular type of enzyme that can break down pectin compounds and is extensively utilised in the agricultural field. In this study, twenty yeast isolates were isolated and assayed for pectinase activity. Molecular identification by PCR amplification and sequencing of internal transcribed spacer (ITS) regions of isolate no. 18 had the highest pectinase activity of 46.35 U/mg, was identified as Rhodotorula mucilaginosa PY18, and was submitted under accession no. (OM275426) in NCBI. Rhodotorula mucilaginosa PY18 was further enhanced through sequential mutagenesis, resulting in a mutant designated as Rhodotorula mucilaginosa E54 with a specific activity of 114.2 U/mg. Using Response Surface Methodology (RSM), the best culture conditions for the pectinase-producing yeast mutant Rhodotorula mucilaginosa E54 were pH 5, 72-h incubation, 2.5% xylose, and 2.5% malt extract, with a pectinase-specific activity of 156.55 U/mg. Then, the obtained sequences of the endo-polygalacturonase PGI gene from Rhodotorula mucilaginosa PY18 and mutant Rhodotorula mucilaginosa E54 were isolated for the first time, sequenced, and submitted to NCBI accession numbers OQ283005 and OQ283006, respectively. The modelled 3D structure of the endo-PGI enzyme (485 residues) was validated using Ramachandran's plot, which showed 87.71, 85.56, and 91.57% in the most favourable region for template Rhodotorula mucilaginosa KR, strain Rhodotorula mucilaginosa PY18, and mutant Rhodotorula mucilaginosa E54, respectively. In molecular docking studies, the results of template Rhodotorula mucilaginosa KR endo-PG1 showed an interaction with an affinity score of - 6.0, - 5.9, and - 5.6 kcal/mol for active sites 1, 2, and 3, respectively. Rhodotorula mucilaginosa PY18 endo-PG1 showed an interaction affinity with a score of - 5.8, - 6.0, and - 5.0 kcal/mol for active sites 1, 2, and 3, respectively. Mutant Rhodotorula mucilaginosa E54 endo-PG1 showed an interaction affinity of - 5.6, - 5.5, - 5.5 and - 5.4 kcal/mol for active sites 1, 2, and 3, respectively. The endo-PGI genes of both the yeast strain Rhodotorula mucilaginosa PY18 and mutant Rhodotorula mucilaginosa E54 were successfully cloned and expressed in E. coli DH5α, showing significantly higher endo-PG1 activity, which recorded 94.57 and 153.10 U/mg for recombinant Rhodotorula mucilaginosa pGEM-PGI-PY18 and recombinant mutant Rhotorula pGEM-PGI-E54, respectively.
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Affiliation(s)
- Nagwa M Abd El-Aziz
- Microbial Genetic Department, Biotechnology Research Institute, National Research Centre, 33 El Buhouth St, Dokki, Cairo, 12622, Egypt.
| | - Maysa E Moharam
- Microbial Chemistry Department, Biotechnology Research Institute, National Research Centre, 33 El Buhouth St, Dokki, Cairo, 12622, Egypt
| | - Nora N El-Gamal
- Microbial Chemistry Department, Biotechnology Research Institute, National Research Centre, 33 El Buhouth St, Dokki, Cairo, 12622, Egypt
| | - Bigad E Khalil
- Microbial Genetic Department, Biotechnology Research Institute, National Research Centre, 33 El Buhouth St, Dokki, Cairo, 12622, Egypt
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Kikiowo B, Ahmad I, Alade AA, T Ijatuyi T, Iwaloye O, Patel HM. Molecular dynamics simulation and pharmacokinetics studies of ombuin and quercetin against human pancreatic α-amylase. J Biomol Struct Dyn 2023; 41:10388-10395. [PMID: 36524470 DOI: 10.1080/07391102.2022.2155699] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 12/01/2022] [Indexed: 12/23/2022]
Abstract
Diabetes mellitus (DM) is a group of metabolic disorders characterised by chronic hyperglycaemia. DM is currently one of the top ten causes of death in humans. Chronic hyperglycaemia in DM leads to long-term damage and failure of different organs in the body. Type 2 DM (T2D) is the most common DM form, characterised by peripheral insulin resistance, relative insulin deficiency, impaired hepatic glucose production regulation and pancreatic β cell dysfunction. The human pancreatic α-amylase (HPA) inhibitor is currently one of the most effective methods developed to inhibit hyperglycaemia in T2D patients. However, the current standard drug available, acarbose, has been associated with severe side effects following prolonged use in patients. Therefore, an alternative drug capable of effectively inhibiting HPA with minimal side effects is required. Based on our previous study, we further explored the therapeutic potential of quercetin and ombuin via molecular dynamics (MD) simulation. The Desmond Simulation Package was used to run 100-ns MD simulations to examine the steady nature and conformational stability of the ligand-HPA complexes. Post-simulation molecular mechanics-generalised born surface area (MM-GBSA) analysis of HPA's binding free energy with quercetin and ombuin was explored. The lead compounds' drug-likeness, absorption, distribution, metabolism and elimination properties were also studied using the SwissADME tool. These results indicate that quercetin and ombuin have great potential as anti-DM drugs with more favourable properties than acarbose.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Babatomiwa Kikiowo
- Department of Biochemistry, Adekunle Ajasin University, Akungba-Akoko, Nigeria
| | - Iqrar Ahmad
- Department of Pharmaceutical Chemistry, Division of Computer-Aided Drug Design, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra, India
| | - Adebowale A Alade
- Department of Biochemistry, Adekunle Ajasin University, Akungba-Akoko, Nigeria
| | - Taiwo T Ijatuyi
- Department of Biochemistry, Adekunle Ajasin University, Akungba-Akoko, Nigeria
| | - Opeyemi Iwaloye
- Bioinformatics and Molecular Biology Unit, Department of Biochemistry, Federal University of Technology Akure, Akure, Ondo State, Nigeria
| | - Harun M Patel
- Department of Pharmaceutical Chemistry, Division of Computer-Aided Drug Design, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra, India
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Abd El-Aziz NM, Khalil BE, El-Gamal NN. Structure prediction, docking studies and molecular cloning of novel Pichia kudriavzevii YK46 metalloprotease (MetPr) for improvement of feather waste biodegradation. Sci Rep 2023; 13:19989. [PMID: 37968282 PMCID: PMC10651840 DOI: 10.1038/s41598-023-47179-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 11/09/2023] [Indexed: 11/17/2023] Open
Abstract
This study addresses the environmental risks associated with the accumulation of keratin waste from poultry, which is resistant to conventional protein degradation methods. To tackle this issue, microbial keratinases have emerged as promising tools for transforming resilient keratin materials into valuable products. We focus on the Metalloprotease (MetPr) gene isolated from novel Pichia kudriavzevii YK46, sequenced, and deposited in the NCBI GenBank database with the accession number OQ511281. The MetPr gene encodes a protein consisting of 557 amino acids and demonstrates a keratinase activity of 164.04 U/ml. The 3D structure of the protein was validated using Ramachandran's plot, revealing that 93% and 97.26% of the 557 residues were situated within the most favoured region for the MetPr proteins of template Pichia kudriavzevii strain 129 and Pichia kudriavzevii YK46, respectively. Computational analyses were employed to determine the binding affinities between the deduced protein and beta keratin. Molecular docking studies elucidated the optimal binding affinities between the metalloprotease (MetPr) and beta-keratin, yielding values of - 260.75 kcal/mol and - 257.02 kcal/mol for the template strains Pichia kudriavzevii strain 129 and Pichia kudriavzevii YK46, respectively. Subsequent molecular cloning and expression of the MetPr gene in E. coli DH5α led to a significantly higher keratinase activity of 281 ± 12.34 U/ml. These findings provide valuable insights into the potential of the MetPr gene and its encoded protein for keratin waste biotransformation, with implications for addressing environmental concerns related to keratinous waste accumulation.
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Affiliation(s)
- Nagwa M Abd El-Aziz
- Microbial Genetic Department, Biotechnology Research Institute, National Research Centre, 33 El Buhouth ST, Dokki, Cairo, 12622, Egypt.
| | - Bigad E Khalil
- Microbial Genetic Department, Biotechnology Research Institute, National Research Centre, 33 El Buhouth ST, Dokki, Cairo, 12622, Egypt
| | - Nora N El-Gamal
- Microbial Chemistry Department, Biotechnology Research Institute, National Research Centre, 33 El Buhouth ST, Dokki, Cairo, 12622, Egypt
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Li C, Yang D, Li L, Wang Y, Chen S, Zhao Y, Lin W. Comparison of the taste mechanisms of umami and bitter peptides from fermented mandarin fish ( Chouguiyu) based on molecular docking and electronic tongue technology. Food Funct 2023; 14:9671-9680. [PMID: 37850257 DOI: 10.1039/d3fo02697c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2023]
Abstract
Unclear taste mechanisms of peptides limit rapid screening of taste peptides with high intensity. In this study, the taste mechanisms of umami and bitter peptides from Chouguiyu were compared. After molecular docking of core umami (NWDDMEK, WFKDEEF, EEEKPKF, DFDDIQK, and DGEKVDF) and bitter (VQDVLKL, VELLKLE, LVVDGVK, VVDLTVR, and VVDGVKL) peptides with T1R1/T1R3 and TASR14, respectively, salt bridges and conventional hydrogen bonds were the main interactions in all taste peptides, in which acidic amino acid residues contributed to the interaction with their receptors. The taste intensity of peptides after solid-phase synthesis was further verified using electronic tongue technology. Spearman correlation analysis showed that docking energy was an important factor for the intensity of taste peptides, while interaction energy and the distance between the binding unit (BU) and the stimulating unit (SU) were also responsible for the bitter intensity. This study provides a theoretical basis to screen novel taste peptides with high taste intensity in fermented foods.
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Affiliation(s)
- Chunsheng Li
- Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs, National R&D Center for Aquatic Product Processing, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China.
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
| | - Daqiao Yang
- Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs, National R&D Center for Aquatic Product Processing, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China.
- College of Life Sciences, Linyi University, Linyi 276000, China
| | - Laihao Li
- Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs, National R&D Center for Aquatic Product Processing, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China.
| | - Yueqi Wang
- Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs, National R&D Center for Aquatic Product Processing, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China.
| | - Shengjun Chen
- Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs, National R&D Center for Aquatic Product Processing, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China.
| | - Yongqiang Zhao
- Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs, National R&D Center for Aquatic Product Processing, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China.
| | - Wanling Lin
- School of Life Science and Food Engineering, Hanshan Normal University, Chaozhou 521041, China
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Loganathan L, Sankar J, Rajendran K, Muthusamy K. Theoretical investigation on known renin inhibitors and generation of ligand-based pharmacophore models for hypertension treatment. J Biomol Struct Dyn 2023:1-10. [PMID: 37897186 DOI: 10.1080/07391102.2023.2275186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 10/20/2023] [Indexed: 10/29/2023]
Abstract
The renin enzyme is considered a promising target for hypertension and renal diseases. Over the last three decades, several experimental and theoretical studies have been engaged in the discovery of potent renin inhibitors. The identified inhibitors that undergo clinical trials are still failing to meet the criteria of potency and safety. To date, there is no specific FDA-approved drug for renin inhibition. Our theoretical opinion describes that the most potent compounds identified in experimental studies but lacking safety and overdose issues could be solved by finding similar molecules that are stable, very active, and have no side effects, which will kick start the drug discovery process. Here, we utilized the most potent direct renin inhibitors reported earlier, followed further by our theoretical study reported in 2019. Ligand-based virtual screening, density functional theory, and dynamic simulation studies were employed to explore the identified compounds and co-crystallized molecule in the protein structure. From the diverse databases, we have identified several identical molecules based on their structural features, such as functional groups like hydrophobic (H), aromatic rings (R), hydrogen bond acceptor (A), and donor (D). The HHHPR five-point pharmacophore feature was identified as a template pharmacophore to search the potential compounds from the Enamine and LifeChemical databases and have a good fitness score with known renin inhibitors. Furthermore, theoretical validation was done through several studies that confirmed the activity of the identified molecules. Overall, we propose that these compounds might break the failure in adverse events and improve the potency of hypertension treatment.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Lakshmanan Loganathan
- Pharmacogenomics and CADD Lab, Department of Bioinformatics, Alagappa University, Karaikudi, India
| | - Jeyanthi Sankar
- Pharmacogenomics and CADD Lab, Department of Bioinformatics, Alagappa University, Karaikudi, India
| | - Kannan Rajendran
- Department of General Medicine, Saveetha Medical College and Hospital, Chennai, India
| | - Karthikeyan Muthusamy
- Pharmacogenomics and CADD Lab, Department of Bioinformatics, Alagappa University, Karaikudi, India
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11
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Jia R, He Y, Liao G, Yang Z, Gu D, Pu Y, Huang M, Wang G. Identification of umami peptides from Wuding chicken by Nano-HPLC-MS/MS and insights into the umami taste mechanisms. Food Res Int 2023; 172:113208. [PMID: 37689849 DOI: 10.1016/j.foodres.2023.113208] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 06/28/2023] [Accepted: 06/29/2023] [Indexed: 09/11/2023]
Abstract
Wuding chicken is popular with consumers in China because of its umami taste. This study aimed to identify novel umami peptides from Wuding chicken and explore the taste mechanism of umami peptides. The molecular masses and amino acid compositions of peptides in Wuding chicken were identified by nano-scale liquid chromatography-tandem mass spectrometry (Nano-HPLC-MS/MS). The taste characteristics of the peptides synthesized by the solid-phase method were evaluated by sensory evaluation combined with electronic tongue technology. The secondary structure of the peptides was further analyzed by circular dichroism (CD), and the relationship between the structure and taste of the peptides was elucidated by molecular docking. The results showed that eight potential umami peptides were identified, among which FVT (FT-3), LDF (LF-3), and DLAGRDLTDYLMKIL (DL-15) had distinct umami tastes, and FT-3 had the highest umami intensity, followed by LF-3 and DL-15. The relative contents of β-sheets in the three umami peptides were 55.20%, 57.30%, and 47.70%, respectively, which were the key components of Wuding chicken umami peptides. In addition to LF-3 embedded in the cavity-binding domain of the TIR1, both FT-3 and DL-15 were embedded in the venus flytrap domain (VFTD) of the T1R3 to bind the umami receptor T1R1/T1R3. The main binding forces between the umami peptides and the umami receptor T1R1/T1R3 relied on hydrogen bonds and hydrophobic interactions, and the key amino acid residues of the combination of umami peptides and the umami receptor T1R1/T1R3 were Glu292, Asn235, and Tyr262.
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Affiliation(s)
- Rong Jia
- College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, China; Livestock Product Processing and Engineering Technology Research Center of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
| | - Ying He
- College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, China; Livestock Product Processing and Engineering Technology Research Center of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
| | - Guozhou Liao
- Livestock Product Processing and Engineering Technology Research Center of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China.
| | - Zijiang Yang
- College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, China; Livestock Product Processing and Engineering Technology Research Center of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
| | - Dahai Gu
- College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, China; Livestock Product Processing and Engineering Technology Research Center of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
| | - Yuehong Pu
- College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, China; Livestock Product Processing and Engineering Technology Research Center of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
| | - Ming Huang
- Key Laboratory of Meat Processing and Quality Control, MOE, Key Laboratory of Meat Processing, MOA, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Guiying Wang
- College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, China; Livestock Product Processing and Engineering Technology Research Center of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China.
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12
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Thirunavukkarasu MK, Karuppasamy R. Drug repurposing combined with MM/PBSA based validation strategies towards MEK inhibitors screening. J Biomol Struct Dyn 2022; 40:12392-12403. [PMID: 34459701 DOI: 10.1080/07391102.2021.1970629] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Emergence of oncogenic mutations in the MAPK pathway gaining more impact in the recent years. Importantly, MEK is a core element of this pathway as it is easy to inhibit and is a gatekeeper of multiple malignancies. Therefore, we performed in-silico strategy to screen repurposed candidate for MEK protein using a library of 11,808 compounds from different clusters in the DrugBank database. Glide docking, Prime-MM/GBSA and QikProp analysis were implemented to retrieve the hits with high precision. The stability of the binding mode and binding affinity of the resultant hit were explored using molecular dynamic simulations and MM/PBSA approach. The results highlight that Nebivolol (DB04861) not only achieved a stable conformation in the MEK binding pocket but also displayed highest binding affinity than the other molecules investigated in our study. Taken together, we hypothesized that Nebivolol is an excellent candidate for the inhibition of MEK in NSCLC patients in future.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Muthu Kumar Thirunavukkarasu
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Ramanathan Karuppasamy
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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Yang D, Li C, Li L, Chen S, Hu X, Xiang H. Taste mechanism of umami peptides from Chinese traditional fermented fish (Chouguiyu) based on molecular docking using umami receptor T1R1/T1R3. Food Chem 2022; 389:133019. [DOI: 10.1016/j.foodchem.2022.133019] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 04/11/2022] [Accepted: 04/18/2022] [Indexed: 01/24/2023]
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Raja A, Shekhar N, Singh H, Prakash A, Medhi B. In-silico discovery of dual active molecule to restore synaptic wiring against autism spectrum disorder via HDAC2 and H3R inhibition. PLoS One 2022; 17:e0268139. [PMID: 35877665 PMCID: PMC9312418 DOI: 10.1371/journal.pone.0268139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 04/22/2022] [Indexed: 11/23/2022] Open
Abstract
Metal-dependent histone deacetylases (HDACs) are essential epigenetic regulators; their molecular and pharmacological roles in medically critical diseases such as neuropsychiatric disorders, neurodegeneration, and cancer are being studied globally. HDAC2’s differential expression in the central nervous system makes it an appealing therapeutic target for chronic neurological diseases like autism spectrum disorder. In this study, we identified H3R inhibitor molecules that are computationally effective at binding to the HDAC2 metal-coordinated binding site. The study highlights the importance of pitolisant in screening the potential H3R inhibitors by using a hybrid workflow of ligand and receptor-based drug discovery. The screened lead compounds with PubChem SIDs 103179850, 103185945, and 103362074 show viable binding with HDAC2 in silico. The importance of ligand contacts with the Zn2+ ion in the HDAC2 catalytic site is also discussed and investigated for a significant role in enzyme inhibition. The proposed H3R inhibitors 103179850, 103185945, and 103362074 are estimated as dual-active molecules to block the HDAC2-mediated deacetylation of the EAAT2 gene (SLC1A2) and H3R-mediated synaptic transmission irregularity and are, therefore, open for experimental validation.
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Affiliation(s)
- Anupam Raja
- Department of Pharmacology, PGIMER, Chandigarh, India
| | | | | | - Ajay Prakash
- Department of Pharmacology, PGIMER, Chandigarh, India
| | - Bikash Medhi
- Department of Pharmacology, PGIMER, Chandigarh, India
- * E-mail:
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Vasudevan A, Kesavan DK, Wu L, Su Z, Wang S, Ramasamy MK, Hopper W, Xu H, Wan C. In Silico and In Vitro Screening of Natural Compounds as Broad-Spectrum β-Lactamase Inhibitors against Acinetobacter baumannii New Delhi Metallo-β-lactamase-1 (NDM-1). BioMed Research International 2022; 2022:1-19. [PMID: 35372567 PMCID: PMC8966755 DOI: 10.1155/2022/4230788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 02/10/2022] [Accepted: 02/17/2022] [Indexed: 11/18/2022]
Abstract
Antibiotic resistance is one of the significant problems globally; there is an increase in resistance with introducing every new class of antibiotics. Further, this has become one of the reasons for arising of new resistance mechanisms in Acinetobacter baumannii. In this study, we have screened natural compounds as a possible inhibitor against the NDM-1 β-lactamase enzyme from A. baumannii using a combination of in silico methods and in vitro evaluation. The database of natural compounds was screened against NDM-1 protein, using Glide docking, followed by QM-polarised ligand docking (QPLD). When the screened hits were validated in vitro, withaferin A and mangiferin had good IC50 values in reducing the activity of NDM-1 enzymes, and their fractional inhibitory concentration index (FICI) was ascertained in combination with imipenem. The withaferin A and mangiferin-NDM-1 docking complexes were analyzed for structural stability by molecular dynamic simulation analysis using GROMACS for 100 ns. The molecular properties of the natural compounds were then calculated using density functional theory (DFT). Withaferin A and mangiferin showed promising inhibitory activity and can be a natural compound candidate inhibitor synergistically used along with carbapenems against NDM-1 producing A. baumannii.
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16
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Thirunavukkarasu MK, Suriya U, Rungrotmongkol T, Karuppasamy R. In Silico Screening of Available Drugs Targeting Non-Small Cell Lung Cancer Targets: A Drug Repurposing Approach. Pharmaceutics 2021; 14:59. [PMID: 35056955 PMCID: PMC8778223 DOI: 10.3390/pharmaceutics14010059] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/16/2021] [Accepted: 12/20/2021] [Indexed: 01/03/2023] Open
Abstract
The RAS-RAF-MEK-ERK pathway plays a key role in malevolent cell progression in many tumors. The high structural complexity in the upstream kinases limits the treatment progress. Thus, MEK inhibition is a promising strategy since it is easy to inhibit and is a gatekeeper for the many malignant effects of its downstream effector. Even though MEK inhibitors are under investigation in many cancers, drug resistance continues to be the principal limiting factor to achieving cures in patients with cancer. Hence, we accomplished a high-throughput virtual screening to overcome this bottleneck by the discovery of dual-targeting therapy in cancer treatment. Here, a total of 11,808 DrugBank molecules were assessed through high-throughput virtual screening for their activity against MEK. Further, the Glide docking, MLSF and prime-MM/GBSA methods were implemented to extract the potential lead compounds from the database. Two compounds, DB012661 and DB07642, were outperformed in all the screening analyses. Further, the study results reveal that the lead compounds also have a significant binding capability with the co-target PIM1. Finally, the SIE-based free energy calculation reveals that the binding of compounds was majorly affected by the van der Waals interactions with MEK receptor. Overall, the in silico binding efficacy of these lead compounds against both MEK and PIM1 could be of significant therapeutic interest to overcome drug resistance in the near future.
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Affiliation(s)
- Muthu Kumar Thirunavukkarasu
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632014, India;
| | - Utid Suriya
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Thanyada Rungrotmongkol
- Biocatalyst and Environmental Biotechnology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand
| | - Ramanathan Karuppasamy
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632014, India;
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Singh KD, Jara ZP, Harford T, Saha PP, Pardhi TR, Desnoyer R, Karnik SS. Novel allosteric ligands of the angiotensin receptor AT1R as autoantibody blockers. Proc Natl Acad Sci U S A 2021; 118:e2019126118. [PMID: 34380734 DOI: 10.1073/pnas.2019126118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
While orthosteric ligands of the angiotensin II (AngII) type 1 receptor (AT1R) are available for clinical and research applications, allosteric ligands are not known for this important G protein-coupled receptor (GPCR). Allosteric ligands are useful tools to modulate receptor pharmacology and subtype selectivity. Here, we report AT1R allosteric ligands for a potential application to block autoimmune antibodies. The epitope of autoantibodies for AT1R is outside the orthosteric pocket in the extracellular loop 2. A molecular dynamics simulation study of AT1R structure reveals the presence of a druggable allosteric pocket encompassing the autoantibody epitope. Small molecule binders were then identified for this pocket using structure-based high-throughput virtual screening. The top 18 hits obtained inhibited the binding of antibody to AT1R and modulated agonist-induced calcium response of AT1R. Two compounds out of 18 studied in detail exerted a negative allosteric modulator effect on the functions of the natural agonist AngII. They blocked antibody-enhanced calcium response and reactive oxygen species production in vascular smooth muscle cells as well as AngII-induced constriction of blood vessels, demonstrating their efficacy in vivo. Our study thus demonstrates the feasibility of discovering inhibitors of the disease-causing autoantibodies for GPCRs. Specifically, for AT1R, we anticipate development of more potent allosteric drug candidates for intervention in autoimmune maladies such as preeclampsia, bilateral adrenal hyperplasia, and the rejection of organ transplants.
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Gupta N, Choudhary SK, Bhagat N, Karthikeyan M, Chaturvedi A. In Silico Prediction, Molecular Docking and Dynamics Studies of Steroidal Alkaloids of Holarrhena pubescens Wall. ex G. Don to Guanylyl Cyclase C: Implications in Designing of Novel Antidiarrheal Therapeutic Strategies. Molecules 2021; 26:4147. [PMID: 34299422 DOI: 10.3390/molecules26144147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 01/08/2023] Open
Abstract
The binding of heat stable enterotoxin (STa) secreted by enterotoxigenic Escherichia coli (ETEC) to the extracellular domain of guanylyl cyclase c (ECDGC-C) causes activation of a signaling cascade, which ultimately results in watery diarrhea. We carried out this study with the objective of finding ligands that would interfere with the binding of STa on ECDGC-C. With this view in mind, we tested the biological activity of a alkaloid rich fraction of Holarrhena pubescens against ETEC under in vitro conditions. Since this fraction showed significant antibacterial activity against ETEC, we decided to test the screen binding affinity of nine compounds of steroidal alkaloid type from Holarrhena pubescens against extracellular domain (ECD) by molecular docking and identified three compounds with significant binding energy. Molecular dynamics simulations were performed for all the three lead compounds to establish the stability of their interaction with the target protein. Pharmacokinetics and toxicity profiling of these leads demonstrated that they possessed good drug-like properties. Furthermore, the ability of these leads to inhibit the binding of STa to ECD was evaluated. This was first done by identifying amino acid residues of ECDGC-C binding to STa by protein-protein docking. The results were matched with our molecular docking results. We report here that holadysenterine, one of the lead compounds that showed a strong affinity for the amino acid residues on ECDGC-C, also binds to STa. This suggests that holadysenterine has the potential to inhibit binding of STa on ECD and can be considered for future study, involving its validation through in vitro assays and animal model studies.
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19
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Loganathan L, Kuriakose BB, Mushfiq S, Muthusamy K. Mechanistic insights on nsSNPs on binding site of renin and cytochrome P450 proteins: A computational perceptual study for pharmacogenomics evaluation. J Cell Biochem 2021; 122:1460-1474. [PMID: 34161641 DOI: 10.1002/jcb.30069] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/24/2021] [Accepted: 05/31/2021] [Indexed: 11/06/2022]
Abstract
Past several decades, therapeutic investigations lead to the discovery of numerous antihypertensive drugs. Although it has been proved for their potency, altered efficacy is common norms in several conditions due to genetic variations. Cytochrome P450 plays a crucial role in drug metabolism and responsible for the pharmacokinetic and pharmacodynamic properties of the drug molecules. Here, we report the deleterious point mutations in the genes associated with the altered response of antihypertensive drug molecules and their metabolizers. Missense variants were filtered as potential nonsynonymous single nucleotide polymorphisms among the available data for the target genes (REN, CYP2D6, CYP3A4). The key objective of the work is to identify the deleterious single nucleotide polymorphisms (SNPs) responsible for the drug response and metabolism for the application of personalized medication. The molecular docking studies revealed that Aliskiren and other clinically approved drug molecules have a high binding affinity with both wild and mutant structures of renin, CYP2D6, and CYP3A4 proteins. The docking (Glide XP) score was observed to have in the range of -8.896 to -11.693 kcal/mol. The molecular dynamics simulation studies were employed to perceive the structural changes and conformational deviation through various analyses. Each studied SNPs was observed to have disparate scoring in the binding affinity to the specific drug molecules. As a prospective plan, we assume this study might be applied to identify the risky SNPs associated with hypertension from the patients to recommend the suitable drug for personalized hypertensive treatment. Further, extensive clinical pharmacogenomics studies are required to support the findings.
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Affiliation(s)
| | - Beena Briget Kuriakose
- Department of Basic Medical Sciences, College of Applied Medical Sciences, King Khalid University, Khamis Mushayt, Saudi Arabia
| | - Sakeena Mushfiq
- Department of Public Health, College of Applied Medical Sciences, King Khalid University, Khamis Mushayt, Saudi Arabia
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Sen D, Bhaumik S, Debnath P, Debnath S. Potentiality of Moringa oleifera against SARS-CoV-2: identified by a rational computer aided drug design method. J Biomol Struct Dyn 2021; 40:7517-7534. [PMID: 33719855 DOI: 10.1080/07391102.2021.1898475] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Coronavirus disease 2019 (COVID-19) has created a global human health crisis and economic setbacks. Lack of specific therapeutics and limited treatment options against COVID-19 has become a new challenge to identify potential hits in order to develop new therapeutics. One of the crucial life cycle enzymes of SARS-CoV-2 is main protease (Mpro), which plays a major role in mediating viral replication, makes it an attractive drug target. Virtual screening and three times repeated 100 ns molecular dynamics simulation of the best hits were performed to identify potential SARS-CoV-2 Mpro inhibitors from the available compounds of an antiviral plant Moringa oleifera. Three flavonoids isorhamnetin (1), kaempferol (2) and apigenin (3) showed good binding affinity, stable protein-ligand complexes throughout the simulation time, high binding energy and similar binding poses in comparison with known SARS-CoV-2 Mpro inhibitor baicalein. Therefore, different parts of M. oleifera may be emerged as a potential preventive and therapeutic against COVID-19.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Debanjan Sen
- Department of Pharmacy, BCDA College of Pharmacy & Technology, Kolkata, West Bengal, India
| | - Samhita Bhaumik
- Department of Chemistry, Women's College, Agartala, Tripura, India
| | - Pradip Debnath
- Department of Chemistry, Maharaja Bir Bikram College, Agartala, Tripura, India
| | - Sudhan Debnath
- Department of Chemistry, Maharaja Bir Bikram College, Agartala, Tripura, India
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21
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Choudhary S, Kumar M, Silakari O. QM/MM analysis, synthesis and biological evaluation of epalrestat based mutual-prodrugs for diabetic neuropathy and nephropathy. Bioorg Chem 2020; 108:104556. [PMID: 33376013 DOI: 10.1016/j.bioorg.2020.104556] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 11/24/2020] [Accepted: 12/10/2020] [Indexed: 10/22/2022]
Abstract
Herein, a quantum mechanics/molecular mechanics (QM/MM) based biotransformation study was performed on synthetically feasible mutual-prodrugs of epalrestat which have been identified from an in-house database developed by us. These prodrugs were submitted to quantum polarized ligand docking (QPLD) with the CES1 enzyme followed by MM-GBSA calculation. Electronic aspects of transition state of these prodrugs were also considered to study the catalytic process through density functional theory (DFT). ADMET analysis of prodrugs was then carried out to assess the drug-likeness. On the basis of in-silico results, the best five prodrugs were synthesized and further evaluated for their neuroprotective and nephroprotective potential in high-fat diet-streptozotocin (HFD-STZ) induced diabetes in rat model. Clinically relevant molecular manifestations of diabetic complications (DC) including aldose reductase (ALR2) activity and oxidative stress markers such as reduced glutathione (GSH), catalase (CAT), and thiobarbituric acid reactive substances (TBARS) were determined in blood plasma as well as tissues of the brain and kidneys. The histopathological examination of these organs was also carried out to see the improvement in structural deformities caused due to neuropathy and nephropathy. Finally, in-vivo pharmacokinetic study was performed for the best two prodrugs to assess the improvement in biopharmaceutical attributes of parent drugs. Overall, EP-G-MFA and EP-MFA have significantly reduced the hyperglycemia-induced ALR2 activity, levels of oxidative stress markers, and manifested about a two-fold increase in the biological half-life (T1/2) of parent drugs. The overall findings of this study suggest that methyl ferulate conjugated prodrugs of epalrestat may be considered as potential protective agents in diabetic neuropathy and nephropathy.
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Affiliation(s)
- Shalki Choudhary
- 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
| | - Om Silakari
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab 147002, India.
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Munni YA, Ali MC, Selsi NJ, Sultana M, Hossen M, Bipasha TH, Rahman M, Uddin MN, Hosen SMZ, Dash R. Molecular simulation studies to reveal the binding mechanisms of shikonin derivatives inhibiting VEGFR-2 kinase. Comput Biol Chem 2020; 90:107414. [PMID: 33191109 DOI: 10.1016/j.compbiolchem.2020.107414] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 10/17/2020] [Accepted: 10/29/2020] [Indexed: 12/20/2022]
Abstract
Traditional vascular endothelial growth factor receptor 2 (VEGFR-2) inhibitors can manage angiogenesis; however, severe toxicity and resistance limit their long-term applications in clinical therapy. Shikonin (SHK) and its derivatives could be promising to inhibit the VEGFR-2 mediated angiogenesis, as they are reported to bind in the catalytic kinase domain with low affinity. However, the detailed molecular insights and binding dynamics of these natural inhibitors are unknown, which is crucial for potential SHK based lead design. Therefore, the present study employed molecular modeling and simulations techniques to get insight into the binding behaviors of SHK and its two derivates, β-hydroxyisovalerylshikonin (β-HIVS) and acetylshikonin (ACS). Here the intermolecular interactions between protein and ligands were studied by induced fit docking approach, which were further evaluated by treating QM/MM (quantum mechanics/molecular mechanics) and molecular dynamics (MD) simulation. The result showed that the naphthazarin ring of the SHK derivates is vital for strong binding to the catalytic domain; however, the binding stability can be modulated by the side chain modification. Because of having electrostatic potential, this ring makes essential interactions with the DFG (Asp1046 and Phe1047) motif and also allows interacting with the allosteric binding site. Taken together, the studies will advance our knowledge and scope for the development of new selective VEGFR-2 inhibitors based on SHK and its analogs.
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Affiliation(s)
- Yeasmin Akter Munni
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju, 38066, Republic of Korea.
| | - Md Chayan Ali
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, 7003, Bangladesh.
| | - Nusrat Jahan Selsi
- Department of Pharmacy, University of Science & Technology, Chittagong, 4202, Bangladesh.
| | - Marium Sultana
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, 4381, Bangladesh.
| | - Md Hossen
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, 4381, Bangladesh.
| | - Tanjiba Harun Bipasha
- Department of Pharmacy, University of Science & Technology, Chittagong, 4202, Bangladesh.
| | - Mahbubur Rahman
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, 4381, Bangladesh.
| | - Md Nazim Uddin
- Department of Pharmacy, Southern University Bangladesh, Chittagong, 4000, Bangladesh.
| | - S M Zahid Hosen
- Pancreatic Research Group, South Western Sydney Clinical School, University of New South Wales, and Ingham Institute for Applied Medical Research, Liverpool, NSW, 2170, Australia.
| | - Raju Dash
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju, 38066, Republic of Korea.
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Kikiowo B, Ogunleye JA, Iwaloye O, Ijatuyi TT. Therapeutic potential of Chromolaena odorata phyto-constituents against human pancreatic α-amylase. J Biomol Struct Dyn 2020; 40:1801-1812. [DOI: 10.1080/07391102.2020.1833758] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Babatomiwa Kikiowo
- Department of Biochemistry, Adekunle Ajasin University, Ondo State, Nigeria
| | | | - Opeyemi Iwaloye
- Federal University of Technology, Akure, Ondo State, Nigeria
| | - Taiwo T. Ijatuyi
- Department of Biochemistry, Adekunle Ajasin University, Ondo State, Nigeria
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24
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Naseri V, Chavoshzadeh Z, Mizani A, Daneshfard B, Ghaffari F, Abbas-Mohammadi M, Gachkar L, Kamalinejad M, Jafari Hajati R, Bahaeddin Z, Faghihzadeh S, Naseri M. Effect of topical marshmallow (Althaea officinalis) on atopic dermatitis in children: A pilot double-blind active-controlled clinical trial of an in-silico-analyzed phytomedicine. Phytother Res 2020; 35:1389-1398. [PMID: 33034099 DOI: 10.1002/ptr.6899] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 09/01/2020] [Accepted: 09/20/2020] [Indexed: 11/11/2022]
Abstract
Atopic dermatitis (AD) is a chronic relapsing eczematous skin disease, which primarily affects infants and young children. Due to the side effects of commonly used drugs for its treatment, the development of safer therapeutic strategies is needed. There are many reports on the topical use of marshmallow (Althaea officinalis) for a range of skin diseases in Persian medicine. The main aim of the present investigation was evaluating the efficacy of marshmallow in children with mild-to-moderate atopic dermatitis. Another aim of the study was screening the anti-allergic and anti-inflammatory potential of phytocomponents against target proteins, including TNF-alpha, IL6, and PDEs A, B, and D enzymes with PDB IDs: 2AZ5, 1P9M, 3I8V, 4KP6, and 1Y2K, respectively, along with their respective standard ligands using computational docking analysis. A pilot clinical trial was designed to investigate the safety and efficacy of Althaea officinalis in children with AD. The diagnosis of AD was made according to the criteria of Hanifin and Rajka. Children between 3 months and 12 years old were participated in this trial and randomly allocated into two parallel intervention and control groups. The intervention group used Althaea officinalis 1% ointment while the positive control group used Hydrocortisone 1% ointment twice a day for a week and after that, three times per week for a period of 3 weeks. The severity of AD was measured using the SCORAD score at the end of each assessment visits. A total number of 22 patients completed the study. A significant decrease of the SCORAD score was observed in both groups. At the end of the study, this score change, which indicates the improvement of the patients was significantly higher in the intervention group in comparison to the baseline (p-value = .015) and week 1 (p-value = .018). In the docking analysis of the study, 33 phytochemical compounds were identified, which were docked into the active site of IL6, TNF-alpha, and human PDE4 isoenzymes. Affinity toward the selected enzymes was significantly higher in glycosylated compounds. The results of this pilot study showed that the efficacy of Althaea officinalis 1% ointment in a decrease of disease severity is more than Hydrocortisone 1% in children with AD. However, further studies are needed to confirm this finding. Moreover, the docking analysis revealed that the inhibitory activity of compounds with free hydroxyl groups such as glycosylated compounds was better than others, probably due to the hydrogen bond interaction of hydroxyl groups of the ligands with the enzymes.
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Affiliation(s)
- Vahedeh Naseri
- Pediatrics Infectious Research Center, Mofid Children's Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zahra Chavoshzadeh
- Pediatrics Infectious Research Center, Mofid Children's Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Allergy and Clinical Immunology, Mofid Children's Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Azadeh Mizani
- Traditional Medicine Clinical Trial Research Center, Shahed University, Tehran, Iran
| | - Babak Daneshfard
- Traditional Medicine Clinical Trial Research Center, Shahed University, Tehran, Iran
| | - Farzaneh Ghaffari
- School of Traditional Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mahdi Abbas-Mohammadi
- Department of Organic Chemistry, Faculty of Chemistry, University of Kashan, Kashan, Iran
| | - Latif Gachkar
- Infectious Disease and Tropical Medicine Reseaerch Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Infectious Diseases Department, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Kamalinejad
- School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Razieh Jafari Hajati
- Traditional Medicine Clinical Trial Research Center, Shahed University, Tehran, Iran
| | - Zahra Bahaeddin
- Traditional Medicine Clinical Trial Research Center, Shahed University, Tehran, Iran
| | - Soghrat Faghihzadeh
- Deptartment of Biostatistics, School of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mohsen Naseri
- Traditional Medicine Clinical Trial Research Center, Shahed University, Tehran, Iran.,Hikmat, Islamic and Traditional Medicine Department, The Academy of Medical Sciences, Tehran, Iran
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25
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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26
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Sarma P, Shekhar N, Prajapat M, Avti P, Kaur H, Kumar S, Singh S, Kumar H, Prakash A, Dhibar DP, Medhi B. In-silico homology assisted identification of inhibitor of RNA binding against 2019-nCoV N-protein (N terminal domain). J Biomol Struct Dyn 2020; 39:2724-2732. [PMID: 32266867 PMCID: PMC7256351 DOI: 10.1080/07391102.2020.1753580] [Citation(s) in RCA: 116] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The N terminal domain (NTD) of Nucleocapsid protein (N protein) of coronavirus (CoV) binds to the viral (+) sense RNA and results in CoV ribonucleoprotien (CoV RNP) complex, essential for the virus replication. In this study, the RNA-binding N terminal domain (NTD) of the N protein was targeted for the identification of possible inhibitors of RNA binding. Two NTD structures of N proteins were selected (2OFZ and 1SSK, 92% homology) for virtual screening of 56,079 compounds from Asinex and Maybridge library to identify top 15 hits for each of the targets based on ‘docking score’. These top-hits were further screened for MM-GBSA binding free energy, pharmacokinetic properties (QikProp) and drug-likeness (SwissADME) and subjected to molecular dynamics (MD) studies. Two suitable binders (ZINC00003118440 and ZINC0000146942) against the target 2OFZ were identified. ZINC00003118440 is a theophylline derivative under the drug class ‘bronchodilators’ and further screening with approved bronchodilators was also studied to identify their ability to bind to the RNA binding region on the N protein. The other identified top hit is ZINC0000146942, which is a 3,4dihydropyrimidone class molecule. Hence this study suggests two important class of compounds, theophylline and pyrimidone derivaties as possible inhibitors of RNA binding to the N terminal domain of N protein of coronavirus, thus opening new avenues for in vitro validations. Communicated by Ramaswamy H. Sarma
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Affiliation(s)
- Phulen Sarma
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Nishant Shekhar
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Manisha Prajapat
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Pramod Avti
- Department of Biophysics, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Hardeep Kaur
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Subodh Kumar
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Sanjay Singh
- Biomedical Informatics Centre, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Harish Kumar
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Ajay Prakash
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Deba Prasad Dhibar
- Internal Medicine, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Bikash Medhi
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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27
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Feng XY, Ding TT, Liu YY, Xu WR, Cheng XC. In-silico identification of peroxisome proliferator-activated receptor (PPAR)α/γ agonists from Ligand Expo Components database. J Biomol Struct Dyn 2020; 39:1853-1864. [DOI: 10.1080/07391102.2020.1745279] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Xiao-Yan Feng
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Ting-Ting Ding
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Ya-Ya Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Wei-Ren Xu
- Tianjin Key Laboratory of Molecular Design and Drug Discovery, Tianjin Institute of Pharmaceutical Research, Tianjin, China
| | - Xian-Chao Cheng
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
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28
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Loganathan L, Gopinath K, Sankaranarayanan VM, Kukreti R, Rajendran K, Lee JK, Muthusamy K. Computational and Pharmacogenomic Insights on Hypertension Treatment: Rational Drug Design and Optimization Strategies. Curr Drug Targets 2019; 21:18-33. [DOI: 10.2174/1389450120666190808101356] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 07/15/2019] [Accepted: 07/16/2019] [Indexed: 02/07/2023]
Abstract
Background::
Hypertension is a prevalent cardiovascular complication caused by genetic
and nongenetic factors. Blood pressure (BP) management is difficult because most patients become
resistant to monotherapy soon after treatment initiation. Although many antihypertensive drugs are
available, some patients do not respond to multiple drugs. Identification of personalized antihypertensive
treatments is a key for better BP management.
Objective::
This review aimed to elucidate aspects of rational drug design and other methods to develop
better hypertension management.
Results::
Among hypertension-related signaling mechanisms, the renin-angiotensin-aldosterone system
is the leading genetic target for hypertension treatment. Identifying a single drug that acts on multiple
targets is an emerging strategy for hypertension treatment, and could be achieved by discovering new
drug targets with less mutated and highly conserved regions. Extending pharmacogenomics research
to include patients with hypertension receiving multiple antihypertensive drugs could help identify the
genetic markers of hypertension. However, available evidence on the role of pharmacogenomics in
hypertension is limited and primarily focused on candidate genes. Studies on hypertension pharmacogenomics
aim to identify the genetic causes of response variations to antihypertensive drugs. Genetic
association studies have identified single nucleotide polymorphisms affecting drug responses. To understand
how genetic traits alter drug responses, computational screening of mutagenesis can be utilized
to observe drug response variations at the protein level, which can help identify new inhibitors
and drug targets to manage hypertension.
Conclusions::
Rational drug design facilitates the discovery and design of potent inhibitors. However,
further research and clinical validation are required before novel inhibitors can be clinically used as
antihypertensive therapies.
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Affiliation(s)
| | - Krishnasamy Gopinath
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul, Korea
| | | | - Ritushree Kukreti
- Genomics and Molecular Medicine Unit, Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research, New Delhi, India
| | - Kannan Rajendran
- Department of General Medicine, Saveetha Medical College and Hospital, Chennai, Tamil Nadu, India
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul, Korea
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Abstract
Structure based drug designing is an important endeavor in the field of structural bioinformatics. Previously the entire process was dependent on the wet-lab experiments to build libraries of ligand molecules. And the molecules used to be tested to determine their binding efficacies with protein target. However, the entire process is very lengthy and above all highly expensive. With the advent of supercomputers and increasing computational powers, the search process for finding suitable ligand molecules against target proteins have become more streamlined and cost-effective. Now the entire ligand search process is performed in-silico with the help of the techniques of virtual screening, molecular docking simulations and molecular dynamics studies. In the present chapter, a brief overview of the computational techniques involved in structure based drug designing is presented with a special emphasis on the thermodynamic principles behind the molecular interactions.
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Affiliation(s)
- Angshuman Bagchi
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, West Bengal, India
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30
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Chen H, Fu W, Wang Z, Wang X, Lei T, Zhu F, Li D, Chang S, Xu L, Hou T. Reliability of Docking-Based Virtual Screening for GPCR Ligands with Homology Modeled Structures: A Case Study of the Angiotensin II Type I Receptor. ACS Chem Neurosci 2019; 10:677-689. [PMID: 30265513 DOI: 10.1021/acschemneuro.8b00489] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The number of solved G-protein-coupled receptor (GPCR) crystal structures has expanded rapidly, but most GPCR structures remain unsolved. Therefore, computational techniques, such as homology modeling, have been widely used to produce the theoretical structures of various GPCRs for structure-based drug design (SBDD). Due to the low sequence similarity shared by the transmembrane domains of GPCRs, accurate prediction of GPCR structures by homology modeling is quite challenging. In this study, angiotensin II type I receptor (AT1R) was taken as a typical case to assess the reliability of class A GPCR homology models for SBDD. Four homology models of angiotensin II type I receptor (AT1R) at the inactive state were built based on the crystal structures of CXCR4 chemokine receptor, CCR5 chemokine receptor, and δ-opioid receptor, and refined through molecular dynamics (MD) simulations and induced-fit docking, to allow for backbone and side-chain flexibility. Then, the quality of the homology models was assessed relative to the crystal structures in terms of two criteria commonly used in SBDD: prediction accuracy of ligand-binding poses and screening power of docking-based virtual screening. It was found that the crystal structures outperformed the homology models prior to any refinement in both assessments. MD simulations could generally improve the docking results for both the crystal structures and homology models. Moreover, the optimized homology model refined by MD simulations and induced-fit docking even shows a similar performance of the docking assessment to the crystal structures. Our results indicate that it is possible to establish a reliable class A GPCR homology model for SBDD through the refinement by integrating multiple molecular modeling techniques.
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Affiliation(s)
| | | | | | | | | | | | | | - Shan Chang
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou 213001, P. R. China
| | - Lei Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou 213001, P. R. China
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31
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Nagamani S, Muthusamy K. A theoretical insight to understand the molecular mechanism of dual target ligand CTA-018 in the chronic kidney disease pathogenesis. PLoS One 2018; 13:e0203194. [PMID: 30286109 PMCID: PMC6171836 DOI: 10.1371/journal.pone.0203194] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 08/16/2018] [Indexed: 11/21/2022] Open
Abstract
The level of the vitamin D in the bloodstream is regulated by cytochrome P450 enzyme 24-hydroxylase A1 (CYP24A1). Over expression of CYP24A1 enzyme is correlated with vitamin D deficiency and resistance to vitamin D therapy. Chronic kidney disease (CKD) patients are commonly reported with the above said expression variations. This deregulation could be solved by ligands that act as a vitamin D receptor (VDR) agonists and CYP24A1 antagonists. Posner et al., (2010) first time reported two new vitamin D analogues namely CTA-091 and CTA-018 to inhibit CYP24A1. The CTA-018 inhibited CYP24A1 with an IC50 27 ± 6 nM (10 times more potent than the ketoconazole (253 ± 20 nM)). CTA-018 induced VDR expression (15-fold lower than 1α,25(OH)2D3) and is under phase II clinical trial, whereas CTA-091 was not able to efficiently induce the VDR expression (>2000 nM). To explore the molecular mechanism, binding specificity of these two vitamin D analogues along with native ligand was extensively studied through in silico approaches. Through molecular dynamics simulations studies, we shown that the sulfonic group (O = S = O) in the side chain of CTA-018 plays an important role in the regulation of VDR agonistic activity. The electron lone pairs of the sulfonic group that interacted with His393 lead to be a factor for agonistic mechanism of VDR activity. Compared to azol-based compounds, CTA-018 binds the different sites in the CYP24A1 binding cavity and thus it could be a potent antagonistic for CYP24A1enzyme.
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32
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Mitra S, Dash R. Structural dynamics and quantum mechanical aspects of shikonin derivatives as CREBBP bromodomain inhibitors. J Mol Graph Model 2018; 83:42-52. [PMID: 29758466 DOI: 10.1016/j.jmgm.2018.04.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 04/16/2018] [Accepted: 04/23/2018] [Indexed: 10/17/2022]
Abstract
The Proteins involved in the chemical modification of lysine residues in histone, is currently being excessively focused as the therapeutic target for the treatment of cell related diseases like cancer. Among these proteins, the epigenetic reader, CREB-binding protein (CREBBP) bromodomain is one of the most prominent targets for effective anticancer drug design, which is responsible for the reorganization of acetylated histone lysine residues. Therefore, this study employed an integrative approach of structure based drug design, in combination with Molecular Dynamics (MD) and QM/MM study to identify as well as to describe the binding mechanism of two shikonin derivatives, acetylshikonin and propionylshikonin as inhibitors of CREBBP bromodomain. Here induced fit docking strategy was employed to explore the important intrinsic interactions of ligands with CREBBP bromodomain, consistently molecular dynamics simulation with two different methods and binding energy calculations by MM-GBSA and MM-PBSA were adopted to determine the stability of intermolecular interactions between protein and ligands. The results showed that both these derivatives made direct contacts with the important conserved residues of the active site, where propionylshikonin demonstrated stronger binding and stability than acetylshikonin, according to molecular dynamics simulation and binding free energy calculations. Further, QM/MM energy calculation was employed to study the chemical reactivity of the propionylshikonin and also to describe the mechanism of non bonded interactions between the propionylshikonin and CREBBP bromodomain. Though this study demands in vitro and in vivo experiments to evaluate the efficiency of the compound, these insights would assist to design more potent CREBBP bromodomain inhibitor, guiding the site of modification of propionylshikonin moiety for designing selective inhibitors.
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Affiliation(s)
- Sarmistha Mitra
- Department of Pharmacy, University of Chittagong, Chittagong, 4331, Bangladesh
| | - Raju Dash
- Molecular Modeling & Drug Design Laboratory (MMDDL), Pharmacology Research Division, Bangladesh Council of Scientific & Industrial Research (BCSIR), Chittagong, 4220, Bangladesh; Department of Biochemistry and Biotechnology, University of Science & Technology Chittagong, Chittagong, 4202, Bangladesh.
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33
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Zhang J, Hao QQ, Liu X, Jing Z, Jia WQ, Wang SQ, Xu WR, Cheng XC, Wang RL. Molecular docking, 3D-QSAR and structural optimization on imidazo-pyridine derivatives dually targeting AT1 and PPARg. Oncotarget 2017; 8:25612-27. [PMID: 28445965 DOI: 10.18632/oncotarget.15778] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 01/27/2017] [Indexed: 12/14/2022] Open
Abstract
Telmisartan, a bifunctional agent of blood pressure lowering and glycemia reduction, was previously reported to antagonize angiotensin II type 1 (AT1) receptor and partially activate peroxisome proliferator-activated receptor γ (PPARγ) simultaneously. Through the modification to telmisartan, researchers designed and obtained imidazo-\pyridine derivatives with the IC50s of 0.49∼94.1 nM against AT1 and EC50s of 20∼3640 nM towards PPARγ partial activation. For minutely inquiring the interaction modes with the relevant receptor and analyzing the structure-activity relationships, molecular docking and 3D-QSAR (Quantitative structure-activity relationships) analysis of these imidazo-\pyridines on dual targets were conducted in this work. Docking approaches of these derivatives with both receptors provided explicit interaction behaviors and excellent matching degree with the binding pockets. The best CoMFA (Comparative Molecular Field Analysis) models exhibited predictive results of q2=0.553, r2=0.954, SEE=0.127, r2pred=0.779 for AT1 and q2=0.503, r2=1.00, SEE=0.019, r2pred=0.604 for PPARγ, respectively. The contour maps from the optimal model showed detailed information of structural features (steric and electrostatic fields) towards the biological activity. Combining the bioisosterism with the valuable information from above studies, we designed six molecules with better predicted activities towards AT1 and PPARγ partial activation. Overall, these results could be useful for designing potential dual AT1 antagonists and partial PPARγ agonists.
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34
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Hadianawala M, Mahapatra AD, Yadav JK, Datta B. Molecular docking, molecular modeling, and molecular dynamics studies of azaisoflavone as dual COX-2 inhibitors and TP receptor antagonists. J Mol Model 2018; 24:69. [DOI: 10.1007/s00894-018-3620-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 02/11/2018] [Indexed: 10/17/2022]
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35
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Muthusamy K, Nagamani S. Vitamin D receptor (VDR) non-synonymous single nucleotide polymorphisms (nsSNPs) affect the calcitriol drug response - A theoretical insight. J Mol Graph Model 2018; 81:14-24. [PMID: 29476931 DOI: 10.1016/j.jmgm.2018.02.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 12/30/2017] [Accepted: 02/05/2018] [Indexed: 11/19/2022]
Abstract
Pharmacogenetics and pharmacogenomics have become presumptive with advancements in next-generation sequencing technology. In complex diseases, distinguishing the feasibility of pathogenic and neutral disease-causing variants is a time consuming and expensive process. Recent drug research and development processes mainly rely on the relationship between the genotype and phenotype through Single nucleotide polymorphisms (SNPs). The SNPs play an indispensable role in elucidating the individual's vulnerability to disease and drug response. The understanding of the interplay between these leads to the establishment of personalized medicine. In order to address this issue, we developed a computational pipeline of vitamin D receptor (VDR) for SNP centered study by application of elegant molecular docking and molecular dynamics simulation approaches. In a few SNPs the volume of the binding cavities has increased in mutant structures when compared to the wild type, indicating a weakening in interaction (699.1 Å3 in wild type Vs. 738.8 in Leu230Val, 820.7 Å3 in Arg247Leu). This also differently reflected in the H-bond interactions and binding free energies -169.93 kcal/mol (wild type) Vs -156.43 kcal/mol (R154W), -105.49 kcal/mol (R274L) in Leu230Val and Arg247Leu respectively. Although we could not find noteworthy changes in the binding free energies and binding pocket in the remaining mutations, the H-bond interactions made these SNPs deleterious. Thus, we further analyzed the H-bond interactions and distances using molecular dynamics (MD) simulation studies.
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Affiliation(s)
| | - Selvaraman Nagamani
- Department of Bioinformatics, Alagappa University, Karaikudi, 630 004, India
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Ganai SA, Abdullah E, Rashid R, Altaf M. Combinatorial In Silico Strategy towards Identifying Potential Hotspots during Inhibition of Structurally Identical HDAC1 and HDAC2 Enzymes for Effective Chemotherapy against Neurological Disorders. Front Mol Neurosci 2017; 10:357. [PMID: 29170627 PMCID: PMC5684606 DOI: 10.3389/fnmol.2017.00357] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 10/19/2017] [Indexed: 11/30/2022] Open
Abstract
Histone deacetylases (HDACs) regulate epigenetic gene expression programs by modulating chromatin architecture and are required for neuronal development. Dysregulation of HDACs and aberrant chromatin acetylation homeostasis have been implicated in various diseases ranging from cancer to neurodegenerative disorders. Histone deacetylase inhibitors (HDACi), the small molecules interfering HDACs have shown enhanced acetylation of the genome and are gaining great attention as potent drugs for treating cancer and neurodegeneration. HDAC2 overexpression has implications in decreasing dendrite spine density, synaptic plasticity and in triggering neurodegenerative signaling. Pharmacological intervention against HDAC2 though promising also targets neuroprotective HDAC1 due to high sequence identity (94%) with former in catalytic domain, culminating in debilitating off-target effects and creating hindrance in the defined intervention. This emphasizes the need of designing HDAC2-selective inhibitors to overcome these vicious effects and for escalating the therapeutic efficacy. Here we report a top-down combinatorial in silico approach for identifying the structural variants that are substantial for interactions against HDAC1 and HDAC2 enzymes. We used extra-precision (XP)-molecular docking, Molecular Mechanics Generalized Born Surface Area (MMGBSA) for predicting affinity of inhibitors against the HDAC1 and HDAC2 enzymes. Importantly, we employed a novel in silico strategy of coupling the state-of-the-art molecular dynamics simulation (MDS) to energetically-optimized structure based pharmacophores (e-Pharmacophores) method via MDS trajectory clustering for hypothesizing the e-Pharmacophore models. Further, we performed e-Pharmacophores based virtual screening against phase database containing millions of compounds. We validated the data by performing the molecular docking and MM-GBSA studies for the selected hits among the retrieved ones. Our studies attributed inhibitor potency to the ability of forming multiple interactions and infirm potency to least interactions. Moreover, our studies delineated that a single HDAC inhibitor portrays differential features against HDAC1 and HDAC2 enzymes. The high affinity and selective HDAC2 inhibitors retrieved through e-Pharmacophores based virtual screening will play a critical role in ameliorating neurodegenerative signaling without hampering the neuroprotective isoform (HDAC1).
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Affiliation(s)
- Shabir Ahmad Ganai
- Chromatin and Epigenetics Lab, Department of Biotechnology, University of Kashmir, Srinagar, India
| | - Ehsaan Abdullah
- Chromatin and Epigenetics Lab, Department of Biotechnology, University of Kashmir, Srinagar, India
| | - Romana Rashid
- Chromatin and Epigenetics Lab, Department of Biotechnology, University of Kashmir, Srinagar, India
| | - Mohammad Altaf
- Chromatin and Epigenetics Lab, Department of Biotechnology, University of Kashmir, Srinagar, India
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Jia WQ, Jing Z, Liu X, Feng XY, Liu YY, Wang SQ, Xu WR, Liu JW, Cheng XC. Virtual identification of novel PPARα/γ dual agonists by scaffold hopping of saroglitazar. J Biomol Struct Dyn 2017; 36:3496-3512. [DOI: 10.1080/07391102.2017.1392363] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Wen-Qing Jia
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Zhi Jing
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Xin Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Xiao-Yan Feng
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Ya-Ya Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Shu-Qing Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Wei-Ren Xu
- Tianjin Key Laboratory of Molecular Design and Drug Discovery, Tianjin Institute of Pharmaceutical Research, Tianjin, China
| | - Jian-Wen Liu
- State Key Laboratory of Bioreactor Engineering & Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Xian-Chao Cheng
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
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Gupta S, Tewatia P, Misri J, Singh R. Molecular Modeling of Cloned Bacillus subtilis Keratinase and Its Insinuation in Psoriasis Treatment Using Docking Studies. Indian J Microbiol 2017; 57:485-491. [PMID: 29151650 DOI: 10.1007/s12088-017-0677-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 09/19/2017] [Indexed: 12/13/2022] Open
Abstract
Present study demonstrated the expression of cloned Bacillus subtilis RSE163 keratinase gene and in silico binding affinities of deduced protein with psoriasis topical drugs for systemic absorption and permeation through skin. The ker gene expressed in E. coli showed significantly higher keratinase activity 450 ± 10.43 U representing 1342 bp nucleotides encoding 447 amino acids with molecular weight of 46 kDa. The modeled structure was validated using ramachandran's plot showing 305 residues (84.3%) in most favoured region. Docking studies using extra precision (XP) method of Glide showed optimum binding affinities with the drugs Acitretin (- 39.62 kcal/mol), Clobetasol propionate (- 37.90 kcal/mol), Fluticasone (- 38.53 kcal/mol), Desonide (- 32.23 kcal/mol), Anthralin (- 38.04 kcal/mol), Calcipotreine (- 21.55 kcal/mol) and Mometasone (- 28.40 kcal/mol) in comparison to other psoriasis drugs. The results can further be correlated with in vitro enzymatic experiments using keratinase as an effective drug mediator through skin to serve the unmet need of industries.
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Affiliation(s)
- Sonali Gupta
- Amity Institute of Microbial Biotechnology, Amity University Uttar Pradesh, Sector-125, Noida, U.P. India
| | - Parul Tewatia
- School of Computer Science and Communication, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Jyoti Misri
- Division of Animal Science, Indian Council of Agricultural Research, Krishi Bhavan, New Delhi, 110114 India
| | - Rajni Singh
- Amity Institute of Microbial Biotechnology, Amity University Uttar Pradesh, Sector-125, Noida, U.P. India
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Zhang J, Wang XJ, Liu X, Huan Y, Yang MM, Shen ZF, Jia WQ, Jing Z, Wang SQ, Xu WR, Cheng XC, Wang RL. Design, sythesis and evaluation of a series of 3- or 4-alkoxy substituted phenoxy derivatives as PPARs agonists. Oncotarget 2017; 8:20766-83. [PMID: 28186999 DOI: 10.18632/oncotarget.15198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 01/25/2017] [Indexed: 11/25/2022] Open
Abstract
Peroxisome proliferators-activated receptors (PPARα, γ and δ) are potentially effective targets for Type 2 diabetes mellitus therapy. The severe effects of known glitazones and the successfully approved agents (saroglitazar and lobeglitazone) motivated us to study novelly potent PPARs drugs with improved safety profile. In this work, we received 15 carboxylic acids based on the combination principle to integrate the polar head of bezafibrate with the hydrophobic tail of pioglitazone. Another 12 tetrazoles based on the bioisosterism principle were obtained accordingly. Furthermore, in vitro PPARs transactivation assays on these 3- or 4-alkoxy substituted phenoxy derivatives afforded six compounds. Interactions and binding stability from the docking analysis and 20 ns molecular dynamic simulations confirmed the representative compounds to be suitable and plausible for PPARs pockets. The above-mentioned results demonstrated that the compounds may be used as reference for further optimization for enhanced PPARs activities and wide safety range.
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Krishna S, Shukla S, Lakra AD, Meeran SM, Siddiqi MI. Identification of potent inhibitors of DNA methyltransferase 1 (DNMT1) through a pharmacophore-based virtual screening approach. J Mol Graph Model 2017; 75:174-188. [PMID: 28582695 DOI: 10.1016/j.jmgm.2017.05.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 05/20/2017] [Accepted: 05/22/2017] [Indexed: 02/06/2023]
Abstract
DNA methylation is an epigenetic change that results in the addition of a methyl group at the carbon-5 position of cytosine residues. DNA methyltransferase (DNMT) inhibitors can suppress tumour growth and have significant therapeutic value. However, the established inhibitors are limited in their application due to their substantial cytotoxicity. Additionally, the standard drugs for DNMT inhibition are non-selective cytosine analogues with considerable cytotoxic side-effects. In the present study, we have designed a workflow by integrating various ligand-based and structure-based approaches to discover new agents active against DNMT1. We have derived a pharmacophore model with the help of available DNMT1 inhibitors. Utilising this model, we performed the virtual screening of Maybridge chemical library and the identified hits were then subsequently filtered based on the Naïve Bayesian classification model. The molecules that have returned from this classification model were subjected to ensemble based docking. We have selected 10 molecules for the biological assay by inspecting the interactions portrayed by these molecules. Three out of the ten tested compounds have shown DNMT1 inhibitory activity. These compounds were also found to demonstrate potential inhibition of cellular proliferation in human breast cancer MDA-MB-231 cells. In the present study, we have utilized a multi-step virtual screening protocol to identify inhibitors of DNMT1, which offers a starting point to develop more potent DNMT1 inhibitors as anti-cancer agents.
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Affiliation(s)
- Shagun Krishna
- Molecular & Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, 260031, India
| | - Samriddhi Shukla
- Endocrinology Division, CSIR-Central Drug Research Institute, Lucknow, 260031, India
| | - Amar Deep Lakra
- Endocrinology Division, CSIR-Central Drug Research Institute, Lucknow, 260031, India
| | - Syed Musthapa Meeran
- Endocrinology Division, CSIR-Central Drug Research Institute, Lucknow, 260031, India
| | - Mohammad Imran Siddiqi
- Molecular & Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, 260031, India.
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Kurczab R. The evaluation of QM/MM-driven molecular docking combined with MM/GBSA calculations as a halogen-bond scoring strategy. Acta Crystallogr B Struct Sci Cryst Eng Mater 2017; 73:188-194. [DOI: 10.1107/s205252061700138x] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Accepted: 01/27/2017] [Indexed: 11/10/2022]
Abstract
The combination of quantum mechanics/molecular mechanics-driven (QM/MM) molecular docking with binding free-energy calculations was successfully used to reproduce the X-ray geometries of protein–ligand complexes with halogen bonding. The procedure involves quantum-polarized ligand docking (QPLD) to obtain the QM-derived ligand atomic charges in the protein environment at the B3PW91/cc-pVTZ level and the MM/GBSA (generalized-Born/surface area) algorithm to calculate the binding free energies of resultant complexes. The performance was validated using a set of 106 X-ray complexes and compared with the Glide and AutoDock VinaXB scoring functions in terms of RMSD and the reconstruction of halogen-bond geometry (distance and σ-hole angle). The results revealed that docking and scoring using the QPLD–GBSA procedure outperformed the remaining scoring functions in the majority of instances. Additionally, a comparison of the orientation of the top ranked binding poses calculated using the fixed atomic charges of ligands obtained from force-field parameterization and by QM calculations in the protein environment provides strong evidence that the use of QM-derived charges is significant.
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Zhang J, Liu X, Wang SQ, Liu GY, Xu WR, Cheng XC, Wang RL. Identification of dual ligands targeting angiotensin II type 1 receptor and peroxisome proliferator-activated receptor-γ by core hopping of telmisartan. J Biomol Struct Dyn 2016; 35:2665-2680. [PMID: 27602589 DOI: 10.1080/07391102.2016.1227726] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
It has been reported previously that some angiotensin II receptor blockers not only antagonize angiotensin II type 1 receptor (AT1R), but also exert stimulation in peroxisome proliferator-activated receptor γ (PPARγ) partial activation, among which telmisartan displays the best. Telmisartan has been tested as a bifunctional ligand with antihypertensive and hypoglycemic activity. Aiming at more potent leads with selective AT1R antagonism and PPARγ partial agonism, the three parts of telmisartan including the distal benzimidazole ring, the biphenyl moiety, and the carboxylic acid group experienced modification by core hopping method in our study. The central benzimidazole ring, however, remained intact considering its great affinity toward AT1R and PPARγ. We utilized computational techniques for the sake of details on the binding interactions and conformational stability. Standard precision docking analysis and absorption, distribution, metabolism, excretion, and toxicity prediction received 10 molecules with higher Glide scores, similar interactions, and improved pharmacokinetic profiles compared to telmisartan. Comp#91 with highest scores for AT1R (-11.92 kcal/mol) and PPARγ (-13.88 kcal/mol) exhibited excellent binding modes and pharmacokinetic parameters. Molecular dynamics trajectories on best docking pose of comp#91 confirmed the docking results and verified the conformational stability with both receptors throughout the course of 20-ns simulations. Thus, comp#91 could be identified as a promising lead in the development of dual AT1R antagonist and PPARγ partial agonist against hypertension and type 2 diabetes.
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Affiliation(s)
- Jun Zhang
- a Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy , Tianjin Medical University , Tianjin 300070 , China
| | - Xin Liu
- a Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy , Tianjin Medical University , Tianjin 300070 , China
| | - Shu-Qing Wang
- a Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy , Tianjin Medical University , Tianjin 300070 , China
| | - Gui-You Liu
- a Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy , Tianjin Medical University , Tianjin 300070 , China
| | - Wei-Ren Xu
- b Tianjin Key Laboratory of Molecular Design and Drug Discovery , Tianjin Institute of Pharmaceutical Research , Tianjin 300193 , China
| | - Xian-Chao Cheng
- a Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy , Tianjin Medical University , Tianjin 300070 , China
| | - Run-Ling Wang
- a Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy , Tianjin Medical University , Tianjin 300070 , China
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Tutone M, Chinnici A, Almerico AM, Perricone U, Sutera FM, De Caro V. Design, synthesis and preliminary evaluation of dopamine-amino acid conjugates as potential D1 dopaminergic modulators. Eur J Med Chem 2016; 124:435-444. [PMID: 27597419 DOI: 10.1016/j.ejmech.2016.08.051] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 08/09/2016] [Accepted: 08/22/2016] [Indexed: 12/31/2022]
Abstract
The dopamine-amino acid conjugate DA-Phen was firstly designed to obtain a useful prodrug for the therapy of Parkinson's disease, but experimental evidence shows that it effectively interacts with D1 dopamine receptors (D1DRs), leading to an enhancement in cognitive flexibility and to the development of adaptive strategies in aversive mazes, together with a decrease in despair-like behavior. In this paper, homology modelling, molecular dynamics, and site mapping of D1 receptor were carried out with the aim of further performing docking studies on other dopamine conjugates compared with D1 agonists, in the attempt to identify new compounds with potential dopaminergic activity. Two new conjugates (DA-Trp 2C, and DA-Leu 3C) have been identified as the most promising candidates, and consequently synthesized. Preliminary evaluation in terms of distribution coefficient (DpH7.4), stability in rat brain homogenate, and in human plasma confirmed that DA-Trp (2C), and DA-Leu (3C) could be considered as very valuable candidates for further in vivo studies as new dopaminergic drugs.
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Affiliation(s)
- Marco Tutone
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università di Palermo, Via Archirafi 32, 90123, Palermo, Italy.
| | - Aurora Chinnici
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università di Palermo, Via Archirafi 32, 90123, Palermo, Italy; Humanitas Clinical and Research Center, Via Manzoni 113, 20089, Rozzano, MI, Italy
| | - Anna Maria Almerico
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università di Palermo, Via Archirafi 32, 90123, Palermo, Italy
| | - Ugo Perricone
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università di Palermo, Via Archirafi 32, 90123, Palermo, Italy
| | - Flavia Maria Sutera
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università di Palermo, Via Archirafi 32, 90123, Palermo, Italy; SiSaf Ltd, Innovation Centre, Northern Ireland Science Park, Queen's Island, Belfast, BT3 9DT, UK
| | - Viviana De Caro
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università di Palermo, Via Archirafi 32, 90123, Palermo, Italy
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Muthusamy K, Krishnasamy G. A computational study on role of 6-(hydroxymethyl)-3-[3,4,5-trihydroxy-6-[(3,4,5-trihydroxyoxan-2-yl)oxymethyl]oxan-2-yl]oxyoxane-2,4,5-triol in the regulation of blood glucose level. J Biomol Struct Dyn 2016; 34:2599-2618. [PMID: 26610163 DOI: 10.1080/07391102.2015.1124289] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
6-(hydroxymethyl)-3-[3,4,5-trihydroxy-6-[(3,4,5-trihydroxyoxan-2-yl)oxymethyl]oxan-2-yl]oxyoxane-2,4,5-triol (SID 242078875) was isolated from the fruits of Syzygium densiflorum Wall. ex Wight & Arn (Myrtaceae), which has been traditionally used in the treatment of diabetes by the tribes of The Nilgiris, Tamil Nadu, India. In this study, reverse pharmacophore mapping approach and text-based database search identified the dipeptidyl peptidase-IV, protein-tyrosine phosphatase 1B, phosphoenolpyruvate carboxykinase, glycogen synthase kinase-3β and glucokinase as potential targets of SID 242078875 in diabetes management. Further, molecular docking was performed to predict the binding pose of SID 242078875 in the active site region of the target protein. In addition, dynamic behaviour and stability of protein-ligand complexes were observed for a period of 50 ns through molecular dynamics simulation.
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Affiliation(s)
- Karthikeyan Muthusamy
- a Department of Bioinformatics , Alagappa University , Science Block, Karaikudi , 630 004 Tamil Nadu , India
| | - Gopinath Krishnasamy
- a Department of Bioinformatics , Alagappa University , Science Block, Karaikudi , 630 004 Tamil Nadu , India
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Selvaraman N, Selvam SK, Muthusamy K. The Binding Mode Prediction and Similar Ligand Potency in the Active Site of Vitamin D Receptor with QM/MM Interaction, MESP, and MD Simulation. Chem Biol Drug Des 2016; 88:272-80. [PMID: 26945790 DOI: 10.1111/cbdd.12754] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Revised: 02/01/2016] [Accepted: 02/29/2016] [Indexed: 01/25/2023]
Abstract
Non-secosteroidal ligands are well-known vitamin D receptor (VDR) agonists. In this study, we described a combined QM/MM to define the protein-ligand interaction energy a strong positive correlation in both QM-MM interaction energy and binding free energy against the biological activity. The molecular dynamics simulation study was performed, and specific interactions were extensively studied. The molecular docking results and surface analysis shed light on steric and electrostatic complementarities of these non-secosteroidal ligands to VDR. Finally, the drug likeness properties were also calculated and found within the acceptable range. The results show that bulky group substitutions in side chain decrease the VDR activity, whereas a small substitution increased it. Functional analyses of H393A and H301A mutations substantiate their roles in the VDR agonistic and antagonistic activities. Apart from the His393 and His301, two other amino acids in the hinge region viz. Ser233 and Arg270 acted as an electron donor/acceptor specific to the agonist in the distinct ligand potency. The results from this study disclose the binding mechanism of VDR agonists and structural modifications required to improve the selectivity.
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Affiliation(s)
- Nagamani Selvaraman
- Pharmacogenomics and CADD Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, 630 004, India
| | - Saravana Kumar Selvam
- Pharmacogenomics and CADD Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, 630 004, India
| | - Karthikeyan Muthusamy
- Pharmacogenomics and CADD Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, 630 004, India
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Kellici TF, Tzakos AG, Mavromoustakos T. Rational drug design and synthesis of molecules targeting the angiotensin II type 1 and type 2 receptors. Molecules 2015; 20:3868-97. [PMID: 25738535 PMCID: PMC6272512 DOI: 10.3390/molecules20033868] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 02/06/2015] [Accepted: 02/15/2015] [Indexed: 02/07/2023] Open
Abstract
The angiotensin II (Ang II) type 1 and type 2 receptors (AT1R and AT2R) orchestrate an array of biological processes that regulate human health. Aberrant function of these receptors triggers pathophysiological responses that can ultimately lead to death. Therefore, it is important to design and synthesize compounds that affect beneficially these two receptors. Cardiovascular disease, which is attributed to the overactivation of the vasoactive peptide hormone Αng II, can now be treated with commercial AT1R antagonists. Herein, recent achievements in rational drug design and synthesis of molecules acting on the two AT receptors are reviewed. Quantitative structure activity relationships (QSAR) and molecular modeling on the two receptors aim to assist the search for new active compounds. As AT1R and AT2R are GPCRs and drug action is localized in the transmembrane region the role of membrane bilayers is exploited. The future perspectives in this field are outlined. Tremendous progress in the field is expected if the two receptors are crystallized, as this will assist the structure based screening of the chemical space and lead to new potent therapeutic agents in cardiovascular and other diseases.
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Affiliation(s)
- Tahsin F Kellici
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou 15771, Greece
- Department of Chemistry, University of Ioannina, Ioannina 45110, Greece
| | - Andreas G Tzakos
- Department of Chemistry, University of Ioannina, Ioannina 45110, Greece
| | - Thomas Mavromoustakos
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou 15771, Greece.
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Han XF, Xue WZ, Hao LP, Zhou ZM. Synthesis and biological evaluation of 4′-[(benzimidazol-1-yl) methyl]biphenyl-2-amides as dual angiotensin II and endothelin A receptor antagonists. Med Chem Commun 2015. [DOI: 10.1039/c5md00169b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Discovery of new benzimidazoles as potent dual AT1 and ETA receptor antagonists with the novel N-(1H-tetrazol-5-yl)-amide fragment.
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Affiliation(s)
- Xiao-Feng Han
- R & D Center for Pharmaceticals
- Beijing Institute of Technology
- Beijing 100081
- PR China
| | - Wei-Zhe Xue
- R & D Center for Pharmaceticals
- Beijing Institute of Technology
- Beijing 100081
- PR China
| | - Li-Ping Hao
- R & D Center for Pharmaceticals
- Beijing Institute of Technology
- Beijing 100081
- PR China
| | - Zhi-Ming Zhou
- R & D Center for Pharmaceticals
- Beijing Institute of Technology
- Beijing 100081
- PR China
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48
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Chinnasamy S, Nagamani S, Muthusamy K. Zn2+ion of the snake venom metalloproteinase (SVMP) plays a critical role in ligand binding: a molecular dynamics simulation study. RSC Adv 2015. [DOI: 10.1039/c5ra14693c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Snake venom metalloproteinase (SVMP) is one of the major components of snake venom and it is a root causative agent for edema, local tissue damage, inflammation, blood coagulation and hemorrhage during the snake bite.
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49
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Singh KD, Naveena Q, Karthikeyan M. Jak2 inhibitor – a jackpot for pharmaceutical industries: a comprehensive computational method in the discovery of new potent Jak2 inhibitors. ACTA ACUST UNITED AC 2014; 10:2146-59. [DOI: 10.1039/c4mb00071d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A potent Jak2 inhibitor could solve numerous diseases and so identifying a potent Jak2 inhibitor could be a jackpot for the pharmaceutical industry. Extensive computational analysis was carried out to identify potent Jak2 inhibitors.
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Affiliation(s)
| | - Queen Naveena
- Department of Bioinformatics
- Alagappa University
- Karaikudi – 630 004, India
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