101
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Hashem HE, Nath A, Kumer A. Synthesis, molecular docking, molecular dynamic, quantum calculation, and antibacterial activity of new Schiff base-metal complexes. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131915] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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102
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Boreak N, Bhandi S. In-Silico modulation of Interleukin-8 (IL8) for the therapeutic management of endodontic pulpitis. Saudi J Biol Sci 2022; 29:905-910. [PMID: 35197758 PMCID: PMC8848128 DOI: 10.1016/j.sjbs.2021.10.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/13/2021] [Accepted: 10/04/2021] [Indexed: 11/16/2022] Open
Abstract
Emerging clinical evidences highlight the association of Interleukin-8 (IL8) with endodontic pulpitis. Relatively higher expression of IL8 has been found in the pulp samples of pulpitis patients with moderate/severe pain. It is speculated that IL8 can be considered as a potential target for therapeutics of endodontic pulpitis. A library consisting of 3072 small molecules from the ZINC database was used to identify potential lead molecules with drug-like properties against the IL8. Based on the in-silico structure-assisted drug designing involving molecular docking, MD simulations, and MMPBSA analyses, we found a small molecule ZINC14613097 inhibits IL8. This study provides a new lead molecule than can be further validated in in-vitro, in-vivo, and ongoing clinical studies for the therapeutic management of endodontic pulpitis.
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103
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Targeting Cytotoxin-Associated Antigen A, a Virulent Factor of Helicobacter pylori-Associated Gastric Cancer: Structure-Based In Silico Screening of Natural Compounds. Molecules 2022; 27:molecules27030732. [PMID: 35164000 PMCID: PMC8838247 DOI: 10.3390/molecules27030732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 12/10/2022] Open
Abstract
Gastric cancer is the fifth most frequent cancer and the third major cause of mortality worldwide. Helicobacter pylori, a bacterial infection linked with GC, injects the cytotoxin-associated antigen A (CagA; an oncoprotein) into host cells. When the phosphorylated CagA protein enters the cell, it attaches to other cellular components, interfering with normal cellular signaling pathways. CagA plays an important role in the progression of GC by interacting with phosphatidylserine of the host cell membrane. Therefore, disrupting the CagA-phosphatidylserine connection using small molecules appears to be a promising therapeutic approach. In this report, we screened the natural compounds from ZINC database against the CagA protein using the bioinformatics tools. Hits were initially chosen based on their physicochemical, absorption, distribution, metabolism, excretion, and toxicity (ADMET) characteristics, as well as other drug-like characteristics. To locate safe and effective hits, the PAINS filter, binding affinities estimation, and interaction analysis were used. Three compounds with high binding affinity and specificity for the CagA binding pocket were discovered. The final hits, ZINC153731, ZINC69482055, and ZINC164387, were found to bind strongly with CagA protein, with binding energies of -11.53, -10.67, and -9.21 kcal/mol, respectively, which were higher than that of the control compound (-7.25 kcal/mol). Further, based on binding affinity and interaction pattern, two leads (ZINC153731, ZINC69482055) were chosen for molecular dynamics (MD) simulation analysis. MD results showed that they displayed stability in their vicinity at 100 ns. This study suggested that these compounds could be used as possible inhibitors of CagA protein in the fight against GC. However, additional benchwork tests are required to validate them as CagA protein inhibitors.
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Malik MS, Alsantali RI, Jamal QMS, Seddigi ZS, Morad M, Alsharif MA, Hussein EM, Jassas RS, Al-Rooqi MM, Abduljaleel Z, Babalgith AO, Altass HM, Moussa Z, Ahmed SA. New Imidazole-Based N-Phenylbenzamide Derivatives as Potential Anticancer Agents: Key Computational Insights. Front Chem 2022; 9:808556. [PMID: 35155379 PMCID: PMC8830504 DOI: 10.3389/fchem.2021.808556] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 12/06/2021] [Indexed: 11/30/2022] Open
Abstract
An efficient atom-economical synthetic protocol to access new imidazole-based N-phenylbenzamide derivatives is described. A one-pot three-component reaction was utilized to provide a series of N-phenylbenzamide derivatives in a short reaction time (2–4 h) with an 80–85% yield. The cytotoxic evaluation revealed that derivatives 4e and 4f exhibited good activity, with IC50 values between 7.5 and 11.1 μM against the tested cancer cell lines. Computational studies revealed interesting insights: the docking of the active derivatives (4e and 4f) showed a higher affinity toward the target receptor protein than the control. Molecular dynamic simulations revealed that the active derivatives form stable complexes with the ABL1 kinase protein. Moreover, the ADME and drug-likeness of the derivatives reinforced the potential of the derivatives to be taken up for further development as anticancer agents.
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Affiliation(s)
- M. Shaheer Malik
- Department of Chemistry, Faculty of Applied Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
- *Correspondence: M. Shaheer Malik, Saleh A. Ahmed,
| | - Reem I. Alsantali
- Department of Pharmaceutical Chemistry, College of Pharmacy, Taif University, Taif, Saudi Arabia
| | - Qazi Mohammad Sajid Jamal
- Department of Health Informatics, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah, Saudi Arabia
| | - Zaki S. Seddigi
- Department of Environmental Health, College of Public Health and Health Informatics, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Moataz Morad
- Department of Chemistry, Faculty of Applied Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Meshari A. Alsharif
- Department of Chemistry, Faculty of Applied Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Essam M. Hussein
- Department of Chemistry, Faculty of Applied Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
- Department of Chemistry, Faculty of Science, Assiut University, Assiut, Egypt
| | - Rabab S. Jassas
- Department of Chemistry, Jamoum University College, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Munirah M. Al-Rooqi
- Department of Chemistry, Faculty of Applied Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | | | - Ahmed O. Babalgith
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Hatem M. Altass
- Department of Chemistry, Faculty of Applied Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Ziad Moussa
- Department of Chemistry, College of Science, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Saleh A. Ahmed
- Department of Chemistry, Faculty of Applied Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
- Department of Chemistry, Faculty of Science, Assiut University, Assiut, Egypt
- *Correspondence: M. Shaheer Malik, Saleh A. Ahmed,
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105
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Ahmad V, Ahmad A, Abuzinadah MF, Al-Thawdi S, Yunus G. Methyltransferase as Antibiotics Against Foodborne Pathogens: An In Silico Approach for Exploring Enzyme as Enzymobiotics. Front Genet 2022; 12:800587. [PMID: 35069699 PMCID: PMC8780565 DOI: 10.3389/fgene.2021.800587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 11/17/2021] [Indexed: 11/13/2022] Open
Abstract
The development of resistance in microbes against antibiotics and limited choice for the use of chemical preservatives in food lead the urgent need to search for an alternative to antibiotics. The enzymes are catalytic proteins that catalyze digestion of bacterial cell walls and protein requirements for the survival of the cell. To study methyltransferase as antibiotics against foodborne pathogen, the methyltransferase enzyme sequence was modeled and its interactions were analyzed against a membrane protein of the gram-positive and gram-negative bacteria through in silico protein-protein interactions. The methyltransferase interaction with cellular protein was found to be maximum, due to the maximum PatchDock Score (15808), which was followed by colicin (12864) and amoxicillin (4122). The modeled protein has found to be interact more significantly to inhibit the indicator bacteria than the tested antibiotics and antimicrobial colicin protein. Thus, model enzyme methyltransferase could be used as enzymobiotics. Moreover, peptide sequences similar to this enzyme sequence need to be designed and evaluated against the microbial pathogen.
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Affiliation(s)
- Varish Ahmad
- Health Information Technology Department, Faculty of Applied Studies, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Aftab Ahmad
- Health Information Technology Department, Faculty of Applied Studies, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohammed F. Abuzinadah
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Salwa Al-Thawdi
- Department of Biology, College of Science, University of Bahrain, Sakhir, Bahrain
| | - Ghazala Yunus
- Department of Basic Science, University of Hail, Hail, Saudi Arabia
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106
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Ilyas U, Nazir B, Altaf R, Muhammad SA, Zafar H, Paiva-Santos AC, Abbas M, Duan Y. Investigation of anti-diabetic potential and molecular simulation studies of dihydropyrimidinone derivatives. Front Endocrinol (Lausanne) 2022; 13:1022623. [PMID: 36313779 PMCID: PMC9596752 DOI: 10.3389/fendo.2022.1022623] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 09/22/2022] [Indexed: 11/13/2022] Open
Abstract
In an attempt to find new targets for α-amylase and α-glucosidase for the treatment of type 2 diabetes mellitus, the present study aims in determining the anti-diabetic potential of synthesized dihydropyrimidinone derivatives. The in vitro α-glucosidase and α-amylase inhibitory activity was performed and the molecular docking analysis of the ligand in the active binding site of target protein was determined. The results revealed significant percent inhibition of α-glucosidase by the compound 6-benzyl-4-(4-hydroxyphenyl)-3,4,6,7-tetrahydro-1H-pyrrolo[3,4-d]pyrimidine-2,5-dione (compound A). The active compound showed 81.99% inhibition when compared to standard ascorbic acid having percent inhibition 81.18%. The IC50 of active compound (A) showed to be 1.02 µg/ml. The molecular docking analysis revealed that the ligand bound to the active binding site of protein with the lowest binding energy of -7.9 kcal/mol that was also significantly similar to standard having -7.8 kcal/mol binding energy. The molecular dynamic simulation studies also revealed stable binding of ligand in the active binding site of protein with low RMSD of 1.7 Å similar to the protein RMSD 1.6Å In conclusion, the study revealed a potential new target against α-glucosidase to treat type 2 diabetes mellitus.
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Affiliation(s)
- Umair Ilyas
- Henan Provincial Key Laboratory of Children’s Genetics and Metabolic Diseases, Children’s Hospital Affiliated to Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Riphah Institute of Pharmaceutical Sciences, Riphah International University, Islamabad, Pakistan
| | - Bisma Nazir
- Riphah Institute of Pharmaceutical Sciences, Riphah International University, Islamabad, Pakistan
| | - Reem Altaf
- Department of Pharmacy, Iqra University Islamabad Campus, Islamabad, Pakistan
- *Correspondence: Yongtao Duan, ; Muhammad Abbas, ; Reem Altaf,
| | - Syed Aun Muhammad
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan
| | - Hajra Zafar
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Ana Cláudia Paiva-Santos
- Department of Pharmaceutical Technology, Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
- REQUIMTE/LAQV, Group of Pharmaceutical Technology, Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
| | - Muhammad Abbas
- Riphah Institute of Pharmaceutical Sciences, Riphah International University, Islamabad, Pakistan
- *Correspondence: Yongtao Duan, ; Muhammad Abbas, ; Reem Altaf,
| | - Yongtao Duan
- Henan Provincial Key Laboratory of Children’s Genetics and Metabolic Diseases, Children’s Hospital Affiliated to Zhengzhou University, Zhengzhou University, Zhengzhou, China
- *Correspondence: Yongtao Duan, ; Muhammad Abbas, ; Reem Altaf,
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107
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Lee KE, Bharadwaj S, Sahoo AK, Yadava U, Kang SG. Determination of tyrosinase-cyanidin-3-O-glucoside and (-/+)-catechin binding modes reveal mechanistic differences in tyrosinase inhibition. Sci Rep 2021; 11:24494. [PMID: 34969954 PMCID: PMC8718538 DOI: 10.1038/s41598-021-03569-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 12/06/2021] [Indexed: 12/13/2022] Open
Abstract
Tyrosinase, exquisitely catalyzes the phenolic compounds into brown or black pigment, inhibition is used as a treatment for dermatological or neurodegenerative disorders. Natural products, such as cyanidin-3-O-glucoside and (-/+)-catechin, are considered safe and non-toxic food additives in tyrosinase inhibition but their ambiguous inhibitory mechanism against tyrosinase is still elusive. Thus, we presented the mechanistic insights into tyrosinase with cyanidin-3-O-glucoside and (-/+)-catechin using computational simulations and in vitro assessment. Initial molecular docking results predicted ideal docked poses (- 9.346 to - 5.795 kcal/mol) for tyrosinase with selected flavonoids. Furthermore, 100 ns molecular dynamics simulations and post-simulation analysis of docked poses established their stability and oxidation of flavonoids as substrate by tyrosinase. Particularly, metal chelation via catechol group linked with the free 3-OH group on the unconjugated dihydropyran heterocycle chain was elucidated to contribute to tyrosinase inhibition by (-/+)-catechin against cyanidin-3-O-glucoside. Also, predicted binding free energy using molecular mechanics/generalized Born surface area for each docked pose was consistent with in vitro enzyme inhibition for both mushroom and murine tyrosinases. Conclusively, (-/+)-catechin was observed for substantial tyrosinase inhibition and advocated for further investigation for drug development against tyrosinase-associated diseases.
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Affiliation(s)
- Kyung Eun Lee
- Department of Biotechnology, Institute of Biotechnology, College of Life and Applied Sciences, Yeungnam University, 280 Daehak-Ro, Gyeongsan, 38541, Gyeongbuk, Korea.
- Stemforce, 313 Institute of Industrial Technology, Yeungnam University, 280 Daehak-Ro, Gyeongsan, 38541, Gyeongbuk, Korea.
| | - Shiv Bharadwaj
- Department of Biotechnology, Institute of Biotechnology, College of Life and Applied Sciences, Yeungnam University, 280 Daehak-Ro, Gyeongsan, 38541, Gyeongbuk, Korea.
- Laboratory of Ligand Engineering, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV Research Center, Vestec, Czech Republic.
| | - Amaresh Kumar Sahoo
- Department of Applied Sciences, Indian Institute of Information Technology Allahabad, Allahabad, 211015, Uttar Pradesh, India.
| | - Umesh Yadava
- Department of Physics, Deen Dayal Upadhyay Gorakhpur University, Gorakhpur, India.
| | - Sang Gu Kang
- Department of Biotechnology, Institute of Biotechnology, College of Life and Applied Sciences, Yeungnam University, 280 Daehak-Ro, Gyeongsan, 38541, Gyeongbuk, Korea.
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108
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Muhseen ZT, Ali MH, Jaber NR, Mashrea DS, Alfalki AM, Li G. Determination of Novel Anti-Cancer Agents by Targeting OGG1 Enzyme Using Integrated Bioinformatics Methods. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:13290. [PMID: 34948899 PMCID: PMC8706639 DOI: 10.3390/ijerph182413290] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 12/12/2021] [Accepted: 12/13/2021] [Indexed: 12/18/2022]
Abstract
The 8-oxoguanine DNA glycosylase (OGG1) enzyme is a key DNA glycosylase mediating the excision of 7,8-dihydro-8-oxoguanine (8-oxoG) from DNA molecule to the start base excision repair pathway. The OGG1 glycosylase function depletion has been seen to obstruct pathological conditions such as inflammation, A3 T-cell lymphoblastic acute leukemia growth, and neurodegenerative diseases, thus warranting OGG1 as an attractive anti-cancer enzyme. Herein, we employed several drug libraries intending to screen non-toxic inhibitory molecules against the active pocket of the enzyme that achieved stable binding mode in dynamics. Two anti-cancer compounds ([O-]C1=C(CC2=CC=CC=C2)SC(=[N+]1CC(=O)NC3=NC=C(CC4=CC=CC=C4)S3)S and CCCN(CCC)[S]-(=O)(=O)C1=CC=C(C=C1)C(=O)NNC2=NC3=CC=C(Br)C=C3C(=N2)C4=CC=CC=C4) from Selleckchem.com were identified to occupy the active pocket of OGG1 and bind with greater affinity than Control TH5487. The binding affinity of Top-1 is -11.6 kcal/mol while that of Top-2 is -10.7 kcal/mol in contrast to TH5487 Control (-9 kcal/mol). During molecular dynamic simulations versus time, the said compounds are tightly held by the enzyme with no minor structural deviations reported except flexible loops in particular those present at the N and C-terminal. Both the compounds produced extensive hydrophobic interactions with the enzyme along with stable hydrogen bonding. The docking and molecular dynamics simulations predictions were further validated by molecular mechanics with generalized Born and surface area solvation (MM/GBSA) and Poisson Boltzmann surface area (MM/PBSA), and WaterSwap binding energies that validated strong binding of the compounds to the enzyme. The MM/GBSA binding free energy for Top-1 complex is -28.10 kcal/mol, Top-2 complex is -50.14 kcal/mol) and Control is -46.91 kcal/mol while MM/PBSA value for Top-1, Top-2 and Control is -23.38 kcal/mol, -35.29 kcal/mol and -38.20 kcal/mol, respectively. Computational pharmacokinetics support good druglike candidacy of the compounds with acceptable profile of pharmacokinetics and very little toxicity. All these findings support the notion that the compounds can be used in experiments to test their anti-cancer activities.
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Affiliation(s)
- Ziyad Tariq Muhseen
- School of Life Sciences, Shaanxi Normal University, Xi’an 710062, China;
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, Shaanxi Normal University, Xi’an 710062, China
| | - Mustafa Hussein Ali
- School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China;
| | - Nawar Rushdi Jaber
- Department of Medical Laboratory Techniques, School of Life Sciences, Dijlah University College, Baghdad 00964, Iraq;
| | - Dheyaa Shakir Mashrea
- Educational Directorate of Babylon Province, Ministry of Education, Babylon 51002, Iraq;
| | - Ali Mamoon Alfalki
- Department of Health Professional Graduate, University of New England, Biddeford, Portland, ME 04005, USA;
| | - Guanglin Li
- School of Life Sciences, Shaanxi Normal University, Xi’an 710062, China;
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, Shaanxi Normal University, Xi’an 710062, China
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109
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S El Salamouni N, Buckley BJ, Jiang L, Huang M, Ranson M, Kelso MJ, Yu H. Disruption of Water Networks is the Cause of Human/Mouse Species Selectivity in Urokinase Plasminogen Activator (uPA) Inhibitors Derived from Hexamethylene Amiloride (HMA). J Med Chem 2021; 65:1933-1945. [PMID: 34898192 DOI: 10.1021/acs.jmedchem.1c01423] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The urokinase plasminogen activator (uPA) plays a critical role in tumor cell invasion and migration and is a promising antimetastasis target. 6-Substituted analogues of 5-N,N-(hexamethylene)amiloride (HMA) are potent and selective uPA inhibitors that lack the diuretic and antikaliuretic properties of the parent drug amiloride. However, the compounds display pronounced selectivity for human over mouse uPA, thus confounding interpretation of data from human xenograft mouse models of cancer. Here, computational and experimental findings reveal that residue 99 is a key contributor to the observed species selectivity, whereby enthalpically unfavorable expulsion of a water molecule by the 5-N,N-hexamethylene ring occurs when residue 99 is Tyr (as in mouse uPA). Analogue 7 lacking the 5-N,N-hexamethylene ring maintained similar water networks when bound to human and mouse uPA and displayed reduced selectivity, thus supporting this conclusion. The study will guide further optimization of dual-potent human/mouse uPA inhibitors from the amiloride class as antimetastasis drugs.
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Affiliation(s)
- Nehad S El Salamouni
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia.,Molecular Horizons, University of Wollongong, Wollongong, NSW 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Benjamin J Buckley
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia.,Molecular Horizons, University of Wollongong, Wollongong, NSW 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia.,CONCERT-Translational Cancer Research Centre, Sydney, NSW 2750, Australia
| | - Longguang Jiang
- National Joint Biomedical Engineering Research Centre on Photodynamic Technologies, Fuzhou University, Fujian 350116, China
| | - Mingdong Huang
- National Joint Biomedical Engineering Research Centre on Photodynamic Technologies, Fuzhou University, Fujian 350116, China
| | - Marie Ranson
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia.,Molecular Horizons, University of Wollongong, Wollongong, NSW 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia.,CONCERT-Translational Cancer Research Centre, Sydney, NSW 2750, Australia
| | - Michael J Kelso
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia.,Molecular Horizons, University of Wollongong, Wollongong, NSW 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Haibo Yu
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia.,Molecular Horizons, University of Wollongong, Wollongong, NSW 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
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110
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Hu XL, Shen W, Wang R, Long H, Wang Q, Feng JH, Pham TA, Xiong F, Ye WC, Wang H. Discovery of Eucalyptin C, derived from the fruits of Eucalyptus globulus Labill., as a novel selective PI3Kγ inhibitor for immunosuppressive treatment. Chin J Nat Med 2021; 19:844-855. [PMID: 34844723 DOI: 10.1016/s1875-5364(21)60111-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Indexed: 11/25/2022]
Abstract
The fruits of Eucalyptus globulus Labill. are known to have a plenty of medicinal properties, such as anti-tumor, anti-inflammatory, and immunosuppressive activity. Our previous study found that the phloroglucinol-sesquiterpene adducts in the fruits of E. globulus were immunosuppressive active constituents, especially Eucalyptin C (EuC). Phosphoinositide 3-kinases-γ (PI3Kγ) plays a pivotal role in T cell mediated excessive immune responses. In this study, EuC was first discovered to be a novel selective PI3Kγ inhibitor with an IC50 value of 0.9 μmol·L-1 and selectivity over 40-fold towards the other PI3K isoforms. Molecular docking, molecular dynamics simulation, and cellular thermal shift assay showed that EuC bound to PI3Kγ. Furthermore, EuC suppressed the downstream of PI3Kγ to induce the apoptosis and inhibit the activation of primary spleen cells derived from allergic contact dermatitis mice. This work highlights the role of the fruits of E. globulus as a source of bioactive plant with immunosuppressive activity.
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Affiliation(s)
- Xiao-Long Hu
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Wei Shen
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Rong Wang
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Huan Long
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Quan Wang
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Jia-Hao Feng
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Thi-Anh Pham
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Fei Xiong
- State Key Laboratory of Bioelectronics, Jiangsu Laboratory for Biomaterials and Devices, Southeast University, Nanjing 210009, China
| | - Wen-Cai Ye
- Institute of Traditional Chinese Medicine and Natural Products, Jinan University, Guangzhou 510632, China
| | - Hao Wang
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
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111
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Yang J, Zhang P, Cheng WX, Lu Y, Gang W, Ren G. Exposing structural variations in SARS-CoV-2 evolution. Sci Rep 2021; 11:22042. [PMID: 34764391 PMCID: PMC8586246 DOI: 10.1038/s41598-021-01650-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 10/29/2021] [Indexed: 12/30/2022] Open
Abstract
The mutation of SARS-CoV-2 influences viral function as residue replacements affect both physiochemical properties and folding conformations. Although a large amount of data on SARS-CoV-2 is available, the investigation of how viral functions change in response to mutations is hampered by a lack of effective structural analysis. Here, we exploit the advances of protein structure fingerprint technology to study the folding conformational changes induced by mutations. With integration of both protein sequences and folding conformations, the structures are aligned for SARS-CoV to SARS-CoV-2, including Alpha variant (lineage B.1.1.7) and Delta variant (lineage B.1.617.2). The results showed that the virus evolution with change in mutational positions and physicochemical properties increased the affinity between spike protein and ACE2, which plays a critical role in coronavirus entry into human cells. Additionally, these structural variations impact vaccine effectiveness and drug function over the course of SARS-CoV-2 evolution. The analysis of structural variations revealed how the coronavirus has gradually evolved in both structure and function and how the SARS-CoV-2 variants have contributed to more severe acute disease worldwide.
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Affiliation(s)
- Jiaan Yang
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, Guangdong, China.
- Micro Biotech, Ltd., Shanghai, 200123, China.
| | - Peng Zhang
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, Guangdong, China
| | - Wen Xiang Cheng
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, Guangdong, China
| | - Youyong Lu
- Laboratory of Molecular Oncology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Wu Gang
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Gang Ren
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
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Identification of Potent Natural Resource Small Molecule Inhibitor to Control Vibrio cholera by Targeting Its Outer Membrane Protein U: An In Silico Approach. Molecules 2021; 26:molecules26216517. [PMID: 34770925 PMCID: PMC8588037 DOI: 10.3390/molecules26216517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/14/2021] [Accepted: 10/18/2021] [Indexed: 11/16/2022] Open
Abstract
Vibrio cholerae causes the diarrheal disease cholera which affects millions of people globally. The outer membrane protein U (OmpU) is the outer membrane protein that is most prevalent in V. cholerae and has already been recognized as a critical component of pathogenicity involved in host cell contact and as being necessary for the survival of pathogenic V. cholerae in the host body. Computational approaches were used in this study to screen a total of 37,709 natural compounds from the traditional Chinese medicine (TCM) database against the active site of OmpU. Following a sequential screening of the TCM database, we report three lead compounds-ZINC06494587, ZINC85510056, and ZINC95910434-that bind strongly to OmpU, with binding affinity values of -8.92, -8.12, and -8.78 kcal/mol, which were higher than the control ligand (-7.0 kcal/mol). To optimize the interaction, several 100 ns molecular dynamics simulations were performed, and the resulting complexes were shown to be stable in their vicinity. Additionally, these compounds were predicted to have good drug-like properties based on physicochemical properties and ADMET assessments. This study suggests that further research be conducted on these compounds to determine their potential use as cholera disease treatment.
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113
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Alrumaihi F. A Comprehensive Computational Screening of Phytochemicals Derived from Saudi Medicinal Plants against Human CC Chemokine Receptor 7 to Identify Potential Anti-Cancer Therapeutics. Molecules 2021; 26:6354. [PMID: 34770763 PMCID: PMC8588288 DOI: 10.3390/molecules26216354] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/15/2021] [Accepted: 10/19/2021] [Indexed: 01/03/2023] Open
Abstract
Homeostatic trafficking of immune cells by CC chemokine receptor 7 (CCR7) keeps immune responses and tolerance in a balance. The involvement of this protein in lymph node metastasis in cancer marks CCR7 as a penitential drug target. Using the crystal structure of CCR7, herein, a comprehensive virtual screening study is presented to filter novel strong CCR7 binding phytochemicals from Saudi medicinal plants that have a higher binding affinity for the intracellular allosteric binding pocket. By doing so, three small natural molecules named as Hit-1 (1,8,10-trihydroxy-3-methoxy-6-methylanthracen-9(4H)-one), Hit-2 (4-(3,4-dimethoxybenzyl)-3-(4-hydroxy-3-methoxybenzyl)dihydrofuran-2(3H)-one), and Hit-3 (10-methyl-12,13-dihydro-[1,2]dioxolo[3,4,5-de]furo[3,2-g]isochromeno[4,3-b]chromen-8-ol) are predicted showing strong binding potential for the CC chemokine receptor 7 allosteric pocket. During molecular dynamics simulations, the compounds were observed in the formation of several chemical bonding of short bond distances. Additionally, the molecules remained in strong contact with the active pocket residues and experienced small conformation changes that seemed to be mediated by the CCR7 loops to properly engage the ligands. Two types of binding energy methods (MM/GBPBSA and WaterSwap) were additionally applied to further validate docking and simulation findings. Both analyses complement the good affinity of compounds for CCR7, the electrostatic and van der Waals energies being the most dominant in intermolecular interactions. The active pocket residue's role in compounds binding was further evaluated via alanine scanning, which highlighted their importance in natural compounds binding. Additionally, the compounds fulfilled all drug-like rules: Lipinski, Ghose, Veber, Egan, and Muegge passed many safety parameters, making them excellent anti-cancer candidates for experimental testing.
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Affiliation(s)
- Faris Alrumaihi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
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114
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Alam S, Mohammad T, Padder RA, Hassan MI, Husain M. Thymoquinone and quercetin induce enhanced apoptosis in non-small cell lung cancer in combination through the Bax/Bcl2 cascade. J Cell Biochem 2021; 123:259-274. [PMID: 34636440 DOI: 10.1002/jcb.30162] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 09/22/2021] [Accepted: 09/30/2021] [Indexed: 12/29/2022]
Abstract
The treatments available for non-small cell lung cancer exert various side effects in patients, and the burden of treatment cost is high. Therefore, exploring the alternative system of medicines, including therapies based on natural compounds, has become inevitable in developing anticancer therapeutics. This study used an integrated approach involving in-silico and in-vitro methods to explore natural compounds targeting Bax and Bcl2 for their apoptotic potential. Molecular docking followed by molecular dynamics (MD) simulation of thymoquinone (Tq) and quercetin (Qu) with Bax and Bcl2 were carried out to explore their interactions and stability under explicit solvent conditions. Tq and Qu showed appreciable binding affinities toward Bax (-6.2 and -7.1 kcal/mol, respectively) and Bcl2 (-5.6 and -6.4 kcal/mol, respectively) with well-organized conformational fitting compatibility. The MD simulation results revealed the development of stable complexes maintained by various noncovalent interactions that were preserved throughout the 100 ns trajectories. Further studies with these compounds were carried out using various in-vitro experimental approaches like MTT assay, apoptotic assay, and Western blot. IC50 values of Tq and Qu alone in A549 cells were found to be 45.78 and 35.69 µM, while in combination, it comes down to 22.49 µM, which is quite impressive. Similarly, in apoptosis assay, a combination of Tq and Qu shows 50.9% early apoptosis compared to Tq (40.6%) and Qu (33.3%) when taken alone. These assays signify their apoptotic induction potential, whereas both compounds significantly reduce the expression of antiapoptotic protein Bcl2 and induce proapoptotic Bax, suggestive of sensitizing NSCLS cells toward apoptosis.
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Affiliation(s)
- Shoaib Alam
- Department of Biotechnology, Jamia Millia Islamia, New Delhi, India
| | - Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Rayees A Padder
- Department of Biotechnology, Jamia Millia Islamia, New Delhi, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Mohammad Husain
- Department of Biotechnology, Jamia Millia Islamia, New Delhi, India
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115
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Designing a Multi-Epitope Vaccine against Chlamydia trachomatis by Employing Integrated Core Proteomics, Immuno-Informatics and In Silico Approaches. BIOLOGY 2021; 10:biology10100997. [PMID: 34681096 PMCID: PMC8533590 DOI: 10.3390/biology10100997] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/22/2021] [Accepted: 09/30/2021] [Indexed: 11/17/2022]
Abstract
Chlamydia trachomatis, a Gram-negative bacterium that infects the rectum, urethra, congenital sites, and columnar epithelium of the cervix. It is a major cause of preventable blindness, ectopic pregnancy, and bacterial sexually transmitted infections worldwide. There is currently no licensed multi-epitope vaccination available for this pathogen. This study used core proteomics, immuno-informatics, and subtractive proteomics approaches to identify the best antigenic candidates for the development of a multi-epitope-based vaccine (MEBV). These approaches resulted in six vaccine candidates: Type III secretion system translocon subunit CopD2, SctW family type III secretion system gatekeeper subunit CopN, SycD/LcrH family type III secretion system chaperone Scc2, CT847 family type III secretion system effector, hypothetical protein CTDEC_0668, and CHLPN 76kDa-like protein. A variety of immuno-informatics tools were used to predict B and T cell epitopes from vaccine candidate proteins. An in silico vaccine was developed using carefully selected epitopes (11 CTL, 2 HTL & 10 LBL) and then docked with the MHC molecules (MHC I & MHC II) and human TLR4. The vaccine was coupled with Cholera toxin subunit B (CTB) adjuvant to boost the immune response. Molecular dynamics (MD) simulations, molecular docking, and MMGBSA analysis were carried out to analyze the molecular interactions and binding affinity of MEBV with TLR4 and MHC molecules. To achieve the highest level of vaccine protein expression, the MEBV was cloned and reverse-translated in Escherichia coli. The highest level of expression was achieved, and a CAI score of 0.97 was reported. Further experimental validation of the MEBV is required to prove its efficacy. The vaccine developed will be useful in preventing infections caused by C. trachomatis.
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116
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Moussaoui O, Byadi S, Eddine Hachim M, Sghyar R, Bahsis L, Moslova K, Aboulmouhajir A, Rodi YK, Podlipnik Č, Hadrami EMEL, Chakroune S. Selective synthesis of novel quinolones-amino esters as potential antibacterial and antifungal agents: Experimental, mechanistic study, docking and molecular dynamic simulations. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130652] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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117
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Ali MA, Nath A, Jannat M, Islam MM. Direct Synthesis of Diamides from Dicarboxylic Acids with Amines Using Nb 2O 5 as a Lewis Acid Catalyst and Molecular Docking Studies as Anticancer Agents. ACS OMEGA 2021; 6:25002-25009. [PMID: 34604680 PMCID: PMC8482773 DOI: 10.1021/acsomega.1c04069] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Indexed: 06/13/2023]
Abstract
Several Lewis and Bronsted acid catalysts were tested for the synthesis of some targeted diamides with anticancer activity from dicarboxylic acids and amines under the same reaction condition. Among those catalysts, Nb2O5 showed the highest catalytic activity to the corresponding diamides. Nb2O5 shows water- and base-tolerant properties for which it gives the highest yield of the synthesized products. Here, we present a novel and sustainable method for the direct synthesis of diamides with anticancer activity using a reusable heterogeneous catalyst Nb2O5. A molecular docking study was performed for all of the synthesized compounds with various therapeutical targets of cancer and found that the human epidermal growth factor receptor (HER2) has shown a significant dock score for our synthesized products. After obtaining the best pose from molecular docking, the complex is used for molecular dynamics study by running simulations for 10 ns. The root-mean-square deviations (RMSDs) of α carbon atoms of all systems are analyzed to detect their stability. This method is effective for the direct synthesis of diamides as anticancer agents from dicarboxylic acids and amines using Nb2O5 as a base-tolerant heterogeneous catalyst.
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Affiliation(s)
- Md. Ayub Ali
- Catalysis
and Organic Synthesis Laboratory, Department of Chemistry, Bangladesh University of Engineering and Technology, Dhaka 1000, Bangladesh
| | - Ashutosh Nath
- Computational
Research for Material Science and Drug Discovery Laboratory, Department
of Chemistry, Bangladesh University of Engineering
and Technology, Dhaka1000, Bangladesh
| | - Meshkatun Jannat
- Catalysis
and Organic Synthesis Laboratory, Department of Chemistry, Bangladesh University of Engineering and Technology, Dhaka 1000, Bangladesh
| | - Md. Midul Islam
- Catalysis
and Organic Synthesis Laboratory, Department of Chemistry, Bangladesh University of Engineering and Technology, Dhaka 1000, Bangladesh
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118
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Pathogenic genetic variants from highly connected cancer susceptibility genes confer the loss of structural stability. Sci Rep 2021; 11:19264. [PMID: 34584144 PMCID: PMC8479081 DOI: 10.1038/s41598-021-98547-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 08/25/2021] [Indexed: 01/09/2023] Open
Abstract
Genetic polymorphisms in DNA damage repair and tumor suppressor genes have been associated with increasing the risk of several types of cancer. Analyses of putative functional single nucleotide polymorphisms (SNP) in such genes can greatly improve human health by guiding choice of therapeutics. In this study, we selected nine genes responsible for various cancer types for gene enrichment analysis and found that BRCA1, ATM, and TP53 were more enriched in connectivity. Therefore, we used different computational algorithms to classify the nonsynonymous SNPs which are deleterious to the structure and/or function of these three proteins. The present study showed that the major pathogenic variants (V1687G and V1736G of BRCA1, I2865T and V2906A of ATM, V216G and L194H of TP53) might have a greater impact on the destabilization of the proteins. To stabilize the high-risk SNPs, we performed mutation site-specific molecular docking analysis and validated using molecular dynamics (MD) simulation and molecular mechanics/Poisson Boltzmann surface area (MM/PBSA) studies. Additionally, SNPs of untranslated regions of these genes affecting miRNA binding were characterized. Hence, this study will assist in developing precision medicines for cancer types related to these polymorphisms.
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119
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Petrov D. Perturbation Free-Energy Toolkit: An Automated Alchemical Topology Builder. J Chem Inf Model 2021; 61:4382-4390. [PMID: 34415755 PMCID: PMC8479811 DOI: 10.1021/acs.jcim.1c00428] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Indexed: 11/30/2022]
Abstract
Free-energy calculations play an important role in the application of computational chemistry to a range of fields, including protein biochemistry, rational drug design, or materials science. Importantly, the free-energy difference is directly related to experimentally measurable quantities such as partition and adsorption coefficients, water activity, and binding affinities. Among several techniques aimed at predicting free-energy differences, perturbation approaches, involving the alchemical transformation of one molecule into another through intermediate states, stand out as rigorous methods based on statistical mechanics. However, despite the importance of free-energy calculations, the applicability of the perturbation approaches is still largely impeded by a number of challenges, including the definition of the perturbation path, i.e., alchemical changes leading to the transformation of one molecule to the other. To address this, an automatic perturbation topology builder based on a graph-matching algorithm is developed, which can identify the maximum common substructure (MCS) of two or multiple molecules and provide the perturbation topologies suitable for free-energy calculations using the GROMOS and the GROMACS simulation packages. Various MCS search options are presented leading to alternative definitions of the perturbation pathway. Moreover, perturbation topologies generated using the default multistate MCS search are used to calculate the changes in free energy between lysine and its two post-translational modifications, 3-methyllysine and acetyllysine. The pairwise free-energy calculations performed on this test system led to a cycle closure of 0.5 ± 0.3 and 0.2 ± 0.2 kJ mol-1, with GROMOS and GROMACS simulation packages, respectively. The same relative free energies between the three states are obtained by employing the enveloping distribution sampling (EDS) approach when compared to the pairwise perturbations. Importantly, this toolkit is made available online as an open-source Python package (https://github.com/drazen-petrov/SMArt).
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Affiliation(s)
- Drazen Petrov
- Department of Material Sciences
and Process Engineering, Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences
Vienna, Muthgasse 18, A-1190 Vienna, Austria
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120
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Dushanan R, Weerasinghe S, Dissanayake DP, Senthilnithy R. An In-Silico Approach to Evaluate the Inhibitory Potency of Selected Hydroxamic Acid Derivatives on Zinc-Dependent Histone Deacetylase Enzyme. JOURNAL OF COMPUTATIONAL BIOPHYSICS AND CHEMISTRY 2021. [DOI: 10.1142/s2737416521500356] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Histone deacetylase (HDAC) enzymes modify the histone by removing the acetyl group from the lysine residues, known as histone deacetylation. HDACs have been involved in altering gene expressions, resulting in cancer cells in the body. This study focuses on HDAC inhibitors’ impact on histone deacetylase-like protein (HDLP) stability through computational techniques. Molecular dynamics (MD) analyses were used to examine the atomic-level description of drug binding sites and how the HDAC inhibitors change the HDLP enzyme environment. In this study, two hydroxamic acid-derived inhibitors, such as [Formula: see text]-Carboxycinnamic acid bis-hydroxamide (CBHA) and scriptaid (GCK1026), were selected to examine the inhibition ability in terms with suberanilohydroxamic acid (SAHA) as a reference drug. The crystal structure of the HDLP was downloaded from the Protein Data Bank. The structures of inhibitors were optimized using the G09W package. Docking studies were done by AutoDock-Vina, and the resultant complex was used to initiate MD studies. The trajectories obtained from MD simulation were used to perform the structural analysis. Root-mean-square deviation (RMSD), radius of gyration, hydrogen bond, binding free energy and interaction energy studies revealed that the stability of HDLP-SAHA and HDLP-CBHA is higher than the free HDLP enzyme. The HDLP-CBHA complex shows an increased number of hydrogen bonds (5), high MM-PBSA binding free energy ([Formula: see text][Formula: see text]kJ/mol), high interaction energy ([Formula: see text][Formula: see text]kJ/mol), and an increased number of alpha-helical amino acids (130) compared with HDLP-SAHA. It concluded that the CBHA has the relatively same potential as SAHA to inhibit the HDLP. Consequently, the use of CBHA in clinical application is recommended through this in-silico method.
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Affiliation(s)
- R. Dushanan
- Department of Chemistry, Faculty of Natural Sciences, The Open University of Sri Lanka, Nawala, Nugegoda 10250, Sri Lanka
| | - S. Weerasinghe
- Department of Chemistry, Faculty of Science, University of Colombo, Colombo 00700, Sri Lanka
| | - D. P. Dissanayake
- Department of Chemistry, Faculty of Science, University of Colombo, Colombo 00700, Sri Lanka
| | - R. Senthilnithy
- Department of Chemistry, Faculty of Natural Sciences, The Open University of Sri Lanka, Nawala, Nugegoda 10250, Sri Lanka
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121
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Farrokhzadeh A, Akher FB, Egan TJ. Molecular Mechanism Exploration of Potent Fluorinated PI3K Inhibitors with a Triazine Scaffold: Unveiling the Unusual Synergistic Effect of Pyridine-to-Pyrimidine Ring Interconversion and CF 3 Defluorination. J Phys Chem B 2021; 125:10072-10084. [PMID: 34473499 DOI: 10.1021/acs.jpcb.1c03242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The phosphatidylinostitol-3-kinase (PI3K)/AKT/mammalian target of rapamycin signaling pathway is a vital regulator of cell proliferation, growth, and survival, which is frequently overactivated in many human cancers. To this effect, PI3K, which is an important mediator of this pathway, has been pinpointed as a crucial target in cancer therapy and hence the importance of PI3K inhibitors. It was recently reported that defluorination and pyridine-to-pyrimidine ring interconversion increase the potency of specific small-molecule inhibitors of PI3K. Compound 4, an inhibitor with the difluorinated pyrimidine motif, was found to be eight times more potent against PI3K than compound 1, an inhibitor with the trifluorinated pyridine motif. This observation presents the need to rationally resolve the differential inhibitory mechanisms exhibited by both compounds. In this present work, we employed multiple computational approaches to investigate and distinguish the binding modes of 1 and 4 in addition to the effects they mediate on the secondary structure of PI3K. Likewise, we evaluated two other derivatives, compounds 2 with the difluorinated pyridine motif and 3 with the trifluorinated pyrimidine motif, to investigate the cooperativity effect between the defluorination of CF3 and pyridine-to-pyrimidine ring interconversion. Findings revealed that PI3K, upon interaction with 4, exhibited a series of structural changes that favored the binding of the inhibitor at the active-site region. Furthermore, a positive (synergistic) cooperativity effect was observed between CF3 defluorination and pyridine-to-pyrimidine ring interconversion. Moreover, there was a good correlation between the binding free energy estimated and the biological activity reported experimentally. Energy decomposition analysis revealed that the major contributing force to binding affinity variations between 1 and 4 is the electrostatic energy. Per-residue energy-based hierarchical clustering analysis further identified four hot-spot residues ASP841, TYR867, ASP964, and LYS833 and four warm-spot residues ASP836, SER806, ASP837, and LYS808, which essentially mediate the optimal and higher-affinity binding of compound 4 to PI3K relative to 1. This study therefore provides rational insights into the mechanisms by which 4 exhibited superior PI3K-inhibitory activities over 1, which is vital for future structure-based drug discovery efforts in PI3K targeting.
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Affiliation(s)
| | - Farideh Badichi Akher
- Department of Chemistry, University of Cape Town, Rondebosch, 7701 Cape Town, South Africa.,Department of Computer Science, University of Cape Town, Rondebosch, 7701 Cape Town, South Africa
| | - Timothy J Egan
- Department of Chemistry, University of Cape Town, Rondebosch, 7701 Cape Town, South Africa
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122
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Yang J, Zhang P, Cheng WX, Lu Y, Gang W, Ren G. Exposing Structural Variations in SARS-CoV-2 Evolution. RESEARCH SQUARE 2021. [PMID: 34545355 PMCID: PMC8452101 DOI: 10.21203/rs.3.rs-800496/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The mutation of SARS-CoV-2 influences viral function as residue replacements affect both physiochemical properties and folding conformations. Although a large amount of data on SARS-CoV-2 is available, the investigation of how viral functions change in response to mutations is hampered by a lack of effective structural analysis. Here, we exploit advances in protein structure fingerprint technology to study the folding conformational changes induced by mutations. With the integration of both protein sequences and folding conformations and alignments of SARS-CoV to SARS-CoV-2, the UK variant and India variant, we found that structural variations in the spike protein at the binding interface interacting with ACE2 play a critical role in coronavirus entry into human cells. Additionally, the structural variations impact vaccine effectiveness and drug function over the course of SARS-CoV-2 evolution. The analysis of structural variations revealed how the coronavirus has gradually evolved in both structure and function and how the SARS-CoV-2 variants have contributed to more severe acute disease worldwide.
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123
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Kisten K, Kumalo HM, Machaba KE, Ndagi U, Mhlongo NN. Drug repurposing approach against Mycobacterium tuberculosis Enoyl-[acyl-carrier-protein] reductase: insight from molecular dynamics simulations. MOLECULAR SIMULATION 2021. [DOI: 10.1080/08927022.2021.1968390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Kimona Kisten
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Hezekiel M. Kumalo
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Kgothatso E. Machaba
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Umar Ndagi
- Africa Centre of Excellence for Mycotoxin and Food Safety, Federal University of Technology, Minna, Nigeria
| | - Ndumiso N. Mhlongo
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
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124
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Anjum F, Mohammad T, Almalki AA, Akhtar O, Abdullaev B, Hassan MI. Phytoconstituents and Medicinal Plants for Anticancer Drug Discovery: Computational Identification of Potent Inhibitors of PIM1 Kinase. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2021; 25:580-590. [PMID: 34448628 DOI: 10.1089/omi.2021.0107] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Natural products, medicinal plants, and phytoconstituents serve as important sources and accelerators for anticancer drug discovery, especially when they are combined with virtual screening and molecular simulations against molecular drug targets. Proto-oncogene serine/threonine-protein kinase Pim1 (PIM1) is involved in cell survival and proliferation, with great relevance for oncogenesis. PIM1 plays a major role in the progression of various common complex human cancers, including prostate cancer, acute myeloid leukemia, and other hematopoietic malignancies. The overexpression of PIM1 leads to cancer progression, and thus it is considered as a potential target for drug design and development purposes. Here, we report original in silico findings by employing structure-based virtual screening to discover potential phytoconstituents from the medicinal plants-based compounds, which could inhibit the PIM1 activity, using the IMPPAT (a curated database of Indian Medicinal Plants, Phytochemistry And Therapeutics) database. The initial hits were selected based on their binding affinity toward PIM1 calculated through the molecular docking approach. Subsequently, interaction analyses and molecular dynamics (MD) simulation for 100 ns was carried out to study the conformational dynamics and complex stability of PIM1 with the identified compounds. Importantly, we found that PIM1 forms stable protein-ligand complexes with the phytoconstituents Dehydrotectol and Nordracorubin in particular. Our findings suggest that identified phytoconstituents Dehydrotectol and Nordracorubin bind to PIM1 in ATP-competitive binding mode. These findings and the compounds reported herein warrant further exploration as promising scaffolds for anticancer drug design, discovery, and development.
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Affiliation(s)
- Farah Anjum
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Abdulraheem Ali Almalki
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Omar Akhtar
- Department of Medicine, Tbilisi State Medical University, Tbilisi, Georgia
| | | | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
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125
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Long H, Hu X, Wang B, Wang Q, Wang R, Liu S, Xiong F, Jiang Z, Zhang XQ, Ye WC, Wang H. Discovery of Novel Apigenin-Piperazine Hybrids as Potent and Selective Poly (ADP-Ribose) Polymerase-1 (PARP-1) Inhibitors for the Treatment of Cancer. J Med Chem 2021; 64:12089-12108. [PMID: 34404206 DOI: 10.1021/acs.jmedchem.1c00735] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Poly (ADP-ribose) polymerase-1 (PARP-1) is a potential target for the discovery of chemosensitizers and anticancer drugs. Amentoflavone (AMF) is reported to be a selective PARP-1 inhibitor. Here, structural modifications and trimming of AMF have led to a series of AMF derivatives (9a-h) and apigenin-piperazine/piperidine hybrids (14a-p, 15a-p, 17a-h, and 19a-f), respectively. Among these compounds, 15l exhibited a potent PARP-1 inhibitory effect (IC50 = 14.7 nM) and possessed high selectivity to PARP-1 over PARP-2 (61.2-fold). Molecular dynamics simulation and the cellular thermal shift assay revealed that 15l directly bound to the PARP-1 structure. In in vitro and in vivo studies, 15l showed a potent chemotherapy sensitizing effect against A549 cells and a selective cytotoxic effect toward SK-OV-3 cells through PARP-1 inhibition. 15l·2HCl also displayed good ADME characteristics, pharmacokinetic parameters, and a desirable safety margin. These findings demonstrated that 15l·2HCl may serve as a lead compound for chemosensitizers and the (BRCA-1)-deficient cancer therapy.
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Affiliation(s)
- Huan Long
- State Key Laboratory of Natural Medicines, Department of TCMs Pharmaceuticals, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Xiaolong Hu
- State Key Laboratory of Natural Medicines, Department of TCMs Pharmaceuticals, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Baolin Wang
- State Key Laboratory of Natural Medicines, Department of TCMs Pharmaceuticals, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Quan Wang
- State Key Laboratory of Natural Medicines, Department of TCMs Pharmaceuticals, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Rong Wang
- State Key Laboratory of Natural Medicines, Department of TCMs Pharmaceuticals, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Shumeng Liu
- State Key Laboratory of Natural Medicines, Department of TCMs Pharmaceuticals, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Fei Xiong
- State Key Laboratory of Bioelectronics, Jiangsu Laboratory for Biomaterials and Devices, Southeast University, Nanjing 210009, People's Republic of China
| | - Zhenzhou Jiang
- Jiangsu Key Laboratory of Drug Screening, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Xiao-Qi Zhang
- Institute of Traditional Chinese Medicine and Natural Products, Jinan University, Guangzhou 510632, People's Republic of China
| | - Wen-Cai Ye
- Institute of Traditional Chinese Medicine and Natural Products, Jinan University, Guangzhou 510632, People's Republic of China
| | - Hao Wang
- State Key Laboratory of Natural Medicines, Department of TCMs Pharmaceuticals, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China
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Jamal QMS, Ahmad V, Alharbi AH, Ansari MA, Alzohairy MA, Almatroudi A, Alghamdi S, Alomary MN, AlYahya S, Shesha NT, Rehman S. Therapeutic development by repurposing drugs targeting SARS-CoV-2 spike protein interactions by simulation studies. Saudi J Biol Sci 2021; 28:4560-4568. [PMID: 33935562 PMCID: PMC8079265 DOI: 10.1016/j.sjbs.2021.04.057] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 04/11/2021] [Accepted: 04/20/2021] [Indexed: 12/20/2022] Open
Abstract
The human-to-human transmitted respiratory illness in COVID-19 affected by the pathogenic Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2), which appeared in the last of December 2019 in Wuhan, China, and rapidly spread in many countries. Thereon, based on the urgent need for therapeutic molecules, we conducted in silico based docking and simulation molecular interaction studies on repurposing drugs, targeting SARS-CoV-2 spike protein. Further, the best binding energy of doxorubicin interacting with virus spike protein (PDB: 6VYB) was observed to be -6.38 kcal/mol and it was followed by exemestane and gatifloxacin. The molecular simulation dynamics analysis of doxorubicin, Reference Mean Square Deviation (RMSD), Root Mean Square fluctuation (RMSF), Radius of Gyration (Rg), and formation of hydrogen bonds plot interpretation suggested, a significant deviation and fluctuation of Doxorubicin-Spike RBD complex during the whole simulation period. The Rg analysis has stated that the Doxorubicin-Spike RBD complex was stable during 15,000-35,000 ps MDS. The results have suggested that doxorubicin could inhibit the virus spike protein and prevent the access of the SARS-CoV-2 to the host cell. Thus, in-vitro/in-vivo research on these drugs could be advantageous to evaluate significant molecules that control the COVID-19 disease.
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Affiliation(s)
- Qazi Mohammad Sajid Jamal
- Department of Health Informatics, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah, Saudi Arabia
| | - Varish Ahmad
- Health Information Technology Department, Faculty of Applied Studies, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ali H Alharbi
- Department of Health Informatics, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah, Saudi Arabia
| | - Mohammad Azam Ansari
- Department of Epidemic Disease Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia
| | - Mohammad A Alzohairy
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Qassim 51431, Saudi Arabia
| | - Ahmad Almatroudi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Qassim 51431, Saudi Arabia
| | - Saad Alghamdi
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Mohammad N. Alomary
- National Centre for Biotechnology, King Abdulaziz City for Science and Technology (KACST), P.O. Box 6086, Riyadh 11442, Saudi Arabia
| | - Sami AlYahya
- National Centre for Biotechnology, King Abdulaziz City for Science and Technology (KACST), P.O. Box 6086, Riyadh 11442, Saudi Arabia
| | | | - Suriya Rehman
- Department of Epidemic Disease Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia
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Anjum F, Ali F, Mohammad T, Shafie A, Akhtar O, Abdullaev B, Hassan I. Discovery of Natural Compounds as Potential Inhibitors of Human Carbonic Anhydrase II: An Integrated Virtual Screening, Docking, and Molecular Dynamics Simulation Study. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2021; 25:513-524. [PMID: 34255561 DOI: 10.1089/omi.2021.0059] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Carbonic anhydrase II (CAII) is one of the zinc metalloenzymes that catalyze the reversible hydration of carbon dioxide, leading to the formation of bicarbonate and proton. CAII plays a significant role in health and disease. For example, CAII helps to maintain eye pressure while regulating the pH of the tumor microenvironment, and by extension, contributing to cancer progression. Owing to its remarkable role in cancer, visual health, and other human diseases, CAII can serve as an attractive therapeutic target. We report an original study based on high-throughput virtual screening of natural compounds from the ZINC database in search of potential inhibitors of CAII. We selected the hits based on the physicochemical, absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties, pan-assay interference compound (PAINS) patterns, and interaction analysis. Importantly, two natural compounds were identified, ZINC08918123 and ZINC00952700, bearing considerable affinity and specific interactions to the residues of the CAII-binding pocket with well-organized conformational fitting compatibility. We investigated the conformational dynamics of CAII in complex with the identified compounds through molecular dynamics simulation, which revealed the formation of a stable complex preserved throughout the 100 ns trajectories. The stability of the protein/ligand complexes is maintained by significant numbers of noncovalent interactions throughout the simulations. In conclusion, natural compounds identified in the present study specifically and computer-assisted drug design broadly offer a reliable resource and strategy to discover potential promising therapeutic inhibitors of CAII to cure various cancers and glaucoma after further experimental validation and clinical studies.
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Affiliation(s)
- Farah Anjum
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Fatima Ali
- Department of Biotechnology, Jamia Millia Islamia, New Delhi, India
| | - Taj Mohammad
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Alaa Shafie
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Omar Akhtar
- Department of Medicine, Tbilisi State Medical University, Tbilisi, Georgia
| | | | - Imtaiyaz Hassan
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
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Khan FI, Kang T, Ali H, Lai D. Remdesivir Strongly Binds to RNA-Dependent RNA Polymerase, Membrane Protein, and Main Protease of SARS-CoV-2: Indication From Molecular Modeling and Simulations. Front Pharmacol 2021; 12:710778. [PMID: 34305617 PMCID: PMC8293383 DOI: 10.3389/fphar.2021.710778] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 06/15/2021] [Indexed: 12/28/2022] Open
Abstract
Development of new drugs is a time-taking and expensive process. Comprehensive efforts are being made globally toward the search of therapeutics against SARS-CoV-2. Several drugs such as remdesivir, favipiravir, ritonavir, and lopinavir have been included in the treatment regimen and shown effective results in several cases. Among the existing broad-spectrum antiviral drugs, remdesivir is found to be more effective against SARS-CoV-2. Remdesivir has broad-spectrum antiviral action against many single-stranded RNA viruses including pathogenic SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV). In this study, we proposed that remdesivir strongly binds to membrane protein (Mprotein), RNA-dependent RNA polymerase (RDRP), and main protease (Mprotease) of SARS-CoV-2. It might show antiviral activity by inhibiting more than one target. It has been found that remdesivir binds to Mprotease, Mprotein, and RDRP with -7.8, -7.4, and -7.1 kcal/mol, respectively. The structure dynamics study suggested that binding of remdesivir leads to unfolding of RDRP. It has been found that strong binding of remdesivir to Mprotein leads to decrease in structural deviations and gyrations. Additionally, the average solvent-accessible surface area of Mprotein decreases from 127.17 to 112.12 nm2, respectively. Furthermore, the eigenvalues and the trace of the covariance matrix were found to be low in case of Mprotease-remdesivir, Mprotein-remdesivir, and RDRP-remdesivir. Binding of remdesivir to Mprotease, Mprotein, and RDRP reduces the average motions in protein due to its strong binding. The MMPBSA calculations also suggested that remdesivir has strong binding affinity with Mprotein, Mprotease, and RDRP. The detailed analysis suggested that remdesivir has more than one target of SARS-CoV-2.
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Affiliation(s)
- Faez Iqbal Khan
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China
| | - Tongzhou Kang
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China
| | - Haider Ali
- Faculty of Medicine, International Ala-Too University, Bishkek, Kyrgyzstan
| | - Dakun Lai
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China
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129
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Integrated Core Proteomics, Subtractive Proteomics, and Immunoinformatics Investigation to Unveil a Potential Multi-Epitope Vaccine against Schistosomiasis. Vaccines (Basel) 2021; 9:vaccines9060658. [PMID: 34208663 PMCID: PMC8235758 DOI: 10.3390/vaccines9060658] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/13/2021] [Accepted: 06/15/2021] [Indexed: 12/14/2022] Open
Abstract
Schistosomiasis is a parasitic infection that causes considerable morbidity and mortality in the world. Infections of parasitic blood flukes, known as schistosomes, cause the disease. No vaccine is available yet and thus there is a need to design an effective vaccine against schistosomiasis. Schistosoma japonicum, Schistosoma mansoni, and Schistosoma haematobium are the main pathogenic species that infect humans. In this research, core proteomics was combined with a subtractive proteomics pipeline to identify suitable antigenic proteins for the construction of a multi-epitope vaccine (MEV) against human-infecting Schistosoma species. The pipeline revealed two antigenic proteins-calcium binding and mycosubtilin synthase subunit C-as promising vaccine targets. T and B cell epitopes from the targeted proteins were predicted using multiple bioinformatics and immunoinformatics databases. Seven cytotoxic T cell lymphocytes (CTL), three helper T cell lymphocytes (HTL), and four linear B cell lymphocytes (LBL) epitopes were fused with a suitable adjuvant and linkers to design a 217 amino-acid-long MEV. The vaccine was coupled with a TLR-4 agonist (RS-09; Sequence: APPHALS) adjuvant to enhance the immune responses. The designed MEV was stable, highly antigenic, and non-allergenic to human use. Molecular docking, molecular dynamics (MD) simulations, and molecular mechanics/generalized Born surface area (MMGBSA) analysis were performed to study the binding affinity and molecular interactions of the MEV with human immune receptors (TLR2 and TLR4) and MHC molecules (MHC I and MHC II). The MEV expression capability was tested in an Escherichia coli (strain-K12) plasmid vector pET-28a(+). Findings of these computer assays proved the MEV as highly promising in establishing protective immunity against the pathogens; nevertheless, additional validation by in vivo and in vitro experiments is required to discuss its real immune-protective efficacy.
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130
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Peele KA, Kumar V, Parate S, Srirama K, Lee KW, Venkateswarulu TC. Insilico drug repurposing using FDA approved drugs against Membrane protein of SARS-CoV-2. J Pharm Sci 2021; 110:2346-2354. [PMID: 33684397 PMCID: PMC7934671 DOI: 10.1016/j.xphs.2021.03.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The novel coronavirus (SARS-CoV-2) outbreak has started taking away the millions of lives worldwide. Identification of known and approved drugs against novel coronavirus disease (COVID-19) seems to be an urgent need for the repurposing of the existing drugs. So, here we examined a safe strategy of using approved drugs of SuperDRUG2 database against modeled membrane protein (M-protein) of SARS-CoV-2 which is essential for virus assembly by using molecular docking-based virtual screening. A total of 3639 drugs from SuperDRUG2 database and additionally 14 potential drugs reported against COVID-19 proteins were selected. Molecular docking analyses revealed that nine drugs can bind the active site of M-protein with desirable molecular interactions. We therefore applied molecular dynamics simulations and binding free energy calculation using MM-PBSA to analyze the stability of the compounds. The complexes of M-protein with the selected drugs were simulated for 50 ns and ranked according to their binding free energies. The binding mode of the drugs with M-protein was analyzed and it was observed that Colchicine, Remdesivir, Bafilomycin A1 from COVID-19 suggested drugs and Temozolomide from SuperDRUG2 database displayed desirable molecular interactions and higher binding affinity towards M-protein. Interestingly, Colchicine was found as the top most binder among tested drugs against M-protein. We therefore additionally identified four Colchicine derivatives which can bind efficiently with M-protein and have better pharmacokinetic properties. We recommend that these drugs can be tested further through in vitro studies against SARS-CoV-2 M-protein.
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Affiliation(s)
- K Abraham Peele
- Department of Bio-Technology, Vignan's Foundation for Science, Technology & Research, Vadlamudi, 522213, Andhra Pradesh, India
| | - Vikas Kumar
- Division of Life Science, Department of Bio & Medical Big Data (BK4 Program), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Republic of Korea
| | - Shraddha Parate
- Division of Applied Life Sciences, Gyeongsang National University (GNU), 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Krupanidhi Srirama
- Department of Bio-Technology, Vignan's Foundation for Science, Technology & Research, Vadlamudi, 522213, Andhra Pradesh, India
| | - Keun Woo Lee
- Division of Life Science, Department of Bio & Medical Big Data (BK4 Program), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Republic of Korea.
| | - T C Venkateswarulu
- Department of Bio-Technology, Vignan's Foundation for Science, Technology & Research, Vadlamudi, 522213, Andhra Pradesh, India.
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Jiang H, Xie X, Ban X, Gu Z, Cheng L, Hong Y, Li C, Li Z. Flexible Loop in Carbohydrate-Binding Module 48 Allosterically Modulates Substrate Binding of the 1,4-α-Glucan Branching Enzyme. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:5755-5763. [PMID: 33988022 DOI: 10.1021/acs.jafc.1c00293] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The 1,4-α-glucan branching enzyme (GBE, EC 2.4.1.18) catalyzes the formation of α-1,6 branching points in starch and plays a key role in synthesis. To obtain mechanistic insights into the catalytic action of the enzyme, we first determined the crystal structure of GBE from Rhodothermus obamensis STB05 (RoGBE) to a resolution of 2.39 Å (PDB ID: 6JOY). The structure consists of three domains: domain A, domain C, and the carbohydrate-binding module 48 (CBM48). An engineered truncated mutant lacking the CBM48 domain (ΔCBM48) showed significantly reduced ligand binding affinity and enzyme activity. Comparison of the structures of RoGBE with other GBEs showed that CBM48 of RoGBE had a longer flexible loop. Truncation of the flexible loops resulted in reduced binding affinity and activity, thereby substantiating the importance of the optimum loop structure for catalysis. In essence, our study shows that CBM48, especially the flexible loop, plays an important role in substrate binding and enzymatic activity of RoGBE. Further, based on the structural analysis, kinetics, and activity assays on wild type and mutants, as well as homology modeling, we proposed a mechanistic model (called the "lid model") to illustrate how the flexible loop triggers substrate binding, ultimately leading to catalysis.
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Affiliation(s)
- Haimin Jiang
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
| | - Xiaofang Xie
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
| | - Xiaofeng Ban
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
| | - Zhengbiao Gu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- Collaborative Innovation Center for Food Safety and Quality Control, Jiangnan University, Wuxi 214122, P. R. China
| | - Li Cheng
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- Collaborative Innovation Center for Food Safety and Quality Control, Jiangnan University, Wuxi 214122, P. R. China
| | - Yan Hong
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- Collaborative Innovation Center for Food Safety and Quality Control, Jiangnan University, Wuxi 214122, P. R. China
| | - Caiming Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- Collaborative Innovation Center for Food Safety and Quality Control, Jiangnan University, Wuxi 214122, P. R. China
| | - Zhaofeng Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- Collaborative Innovation Center for Food Safety and Quality Control, Jiangnan University, Wuxi 214122, P. R. China
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132
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Li B, Yao J, He F, Liu J, Lin Z, Liu S, Wang W, Wu T, Huang J, Chen K, Fang M, Chen J, Zeng JZ. Synthesis, SAR study, and bioactivity evaluation of a series of Quinoline-Indole-Schiff base derivatives: Compound 10E as a new Nur77 exporter and autophagic death inducer. Bioorg Chem 2021; 113:105008. [PMID: 34089944 DOI: 10.1016/j.bioorg.2021.105008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 05/08/2021] [Accepted: 05/18/2021] [Indexed: 01/03/2023]
Abstract
We previously reported 5-((8-methoxy-2-methylquinolin-4-yl)amino)-1H-indole- 2-carbohydrazide derivatives as new Nur77 modulators. In this study, we explored whether the 8-methoxy-2-methylquinoline moiety and bicyclic aromatic rings at the N'-methylene position were critical for their antitumor activity against hepatocellular carcinoma (HCC). For this purpose, a small library of 5-substituted 1H-indole-2-carbohydrazide derivatives was designed and synthesized. We found that the 8-methoxy-2-methylquinoline moiety was a fundamental structure for its biological function, while the introduction of the bicyclic aromatic ring into the N'-methylene greatly improved its anti-tumor effect. We found that the representative compound 10E had a high affinity to Nur77. The KD values were in the low micromolar (2.25-4.10 μM), which were coincident with its IC50 values against the tumor cell lines (IC50 < 3.78 μM). Compound 10E could induce autophagic cell death of liver cancer cells by targeting Nur77 to mitochondria while knocking down Nur77 greatly impaired anti-tumor effect. These findings provide an insight into the structure-activity relation of Quinoline-Indole-Schiff base derivatives and further demonstrate that antitumor agents targeting Nur77 may be considered as a promising strategy for HCC therapy.
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Affiliation(s)
- Baicun Li
- School of Pharmaceutical Sciences and School of Public Health, Xiamen University, Xiamen 361102, China; State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Department of Physiology, Peking Union Medical College, Beijing 100730, China
| | - Jie Yao
- School of Pharmaceutical Sciences and School of Public Health, Xiamen University, Xiamen 361102, China; Radiation Oncology Key Laboratory of Sichuan Province, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610000, China
| | - Fengming He
- School of Pharmaceutical Sciences and School of Public Health, Xiamen University, Xiamen 361102, China
| | - Jie Liu
- School of Pharmaceutical Sciences and School of Public Health, Xiamen University, Xiamen 361102, China
| | - Zongxin Lin
- School of Pharmaceutical Sciences and School of Public Health, Xiamen University, Xiamen 361102, China
| | - Shunzhi Liu
- School of Pharmaceutical Sciences and School of Public Health, Xiamen University, Xiamen 361102, China
| | - Wang Wang
- Key Laboratory of Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Tong Wu
- School of Pharmaceutical Sciences and School of Public Health, Xiamen University, Xiamen 361102, China
| | - Jiangang Huang
- School of Pharmaceutical Sciences and School of Public Health, Xiamen University, Xiamen 361102, China
| | - Kun Chen
- School of Pharmaceutical Sciences and School of Public Health, Xiamen University, Xiamen 361102, China
| | - Meijuan Fang
- School of Pharmaceutical Sciences and School of Public Health, Xiamen University, Xiamen 361102, China.
| | - Jingwei Chen
- School of Pharmaceutical Sciences and School of Public Health, Xiamen University, Xiamen 361102, China.
| | - Jin-Zhang Zeng
- School of Pharmaceutical Sciences and School of Public Health, Xiamen University, Xiamen 361102, China.
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133
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Hu XL, Lv XY, Wang R, Long H, Feng JH, Wang BL, Shen W, Liu H, Xiong F, Zhang XQ, Ye WC, Wang H. Optimization of N-Phenylpropenoyl-l-amino Acids as Potent and Selective Inducible Nitric Oxide Synthase Inhibitors for Parkinson's Disease. J Med Chem 2021; 64:7760-7777. [PMID: 34019417 DOI: 10.1021/acs.jmedchem.1c00578] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
N-Phenylpropenoyl-l-amino acids (NPAs) are inducible nitric oxide synthase (iNOS) inhibitors possessing preventive effects for Parkinson's disease (PD). Here, structural modifications for improving the iNOS inhibitory activity and blood-brain barrier (BBB) permeability of NPAs were conducted, leading to 20 optimized NPA derivatives (1-20). Compound 18, with the most potent activity (IC50 = 74 nM), high BBB permeability (Pe = 19.1 × 10-6 cm/s), and high selectivity over other NOS isoforms, was selected as the lead compound. Further studies demonstrated that 18 directly binds to iNOS. In the 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced acute PD model, the oral administration of 18 (1 and 2 mg/kg) exerted preventive effects by alleviating the loss of dopaminergic (DAergic) neurons. Notably, in the MPTP-/probenecid-induced chronic PD model, the same dose of 18 also displayed a therapeutic effect by repairing the damaged DAergic neurons. Finally, good pharmacokinetic properties and low toxicity made 18 a promising candidate for the treatment of PD.
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Affiliation(s)
- Xiao-Long Hu
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Xian-Yu Lv
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Rong Wang
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Huan Long
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Jia-Hao Feng
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Bao-Lin Wang
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Wei Shen
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Hao Liu
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Fei Xiong
- State Key Laboratory of Bioelectronics, Jiangsu Laboratory for Biomaterials and Devices, Southeast University, Nanjing 210009, People's Republic of China
| | - Xiao-Qi Zhang
- Institute of Traditional Chinese Medicine and Natural Products, Jinan University, Guangzhou 510632, People's Republic of China
| | - Wen-Cai Ye
- Institute of Traditional Chinese Medicine and Natural Products, Jinan University, Guangzhou 510632, People's Republic of China
| | - Hao Wang
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China
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134
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Singh AK, Burada PS, Roy A. Biomolecular response to hour-long ultralow field microwave radiation: An effective coarse-grained model simulation. Phys Rev E 2021; 103:042416. [PMID: 34005990 DOI: 10.1103/physreve.103.042416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 03/16/2021] [Indexed: 11/07/2022]
Abstract
Various electronic devices, which we commonly use, radiate microwaves. Such external perturbation influences the functionality of biomolecules. In an ultralow field, the cumulative response of a molecule is expected only over a time scale of hours. To study the structural dynamics of biomolecules over hours, we adopt a simple methodology for constructing the coarse-grained structure of the protein molecule and solve the Langevin equation under different working potentials. In this approach, each amino acid residue of a biomolecule is mapped onto a number of beads, a few for the backbone, and few for the side chain, depending on the complexity of its chemical structure. We choose the force field in such a way that the dynamics of the protein molecule in the presence of ultralow radiation field of microvolt/nm could be followed over the time frame of 2 h. We apply the model to describe a biomolecule, hen egg white lysozyme, and simulate its structural evolution under ultralow strength electromagnetic radiation. The simulation revealed the finer structural details, like the extent of exposure of bioactive residues and the state of the secondary structures of the molecule, further confirmed from spectroscopic measurements [details are available in Phys. Rev. E 97, 052416 (2018)10.1103/PhysRevE.97.052416 and briefly described here]. Though tested for a specific system, the model is quite general. We believe that it harnesses the potential in studying the structural dynamics of any biopolymer under external perturbation over an extended time scale.
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Affiliation(s)
- Anang Kumar Singh
- Department of Physics, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
| | - P S Burada
- Department of Physics, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
| | - Anushree Roy
- Department of Physics, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
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135
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Khan FI, Song H, Hassan F, Tian J, Tang L, Lai D, Juan F. Impact of amino acid substitutions on the behavior of a photoactivatable near infrared fluorescent protein PAiRFP1. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 253:119572. [PMID: 33631627 DOI: 10.1016/j.saa.2021.119572] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 01/16/2021] [Accepted: 01/29/2021] [Indexed: 06/12/2023]
Abstract
A photoactivatable near-infrared fluorescent protein (NIR-FP) PAiRFP1 has been developed by 15 amino acid substitutions in its nonfluorescent template Agp2. In our previous communication, we investigated the role of three amino acids in PHY domain distal from BV molecule. The impact of the twelve amino acids in GAF domain, especially five residues near BV-binding pocket is unclear. In this paper, PCR based reverse mutagenesis, spectroscopic methods, molecular modelling and simulations have been employed to explore the roles of these substitutions during the molecular evolution of PAiRFP1. It was found that the residue L163 is important for protein folding in PAiRFP1. The residues F244 and C280 exerted remarkable effects on molar extinction coefficient, NIR fluorescence quantum yield, molecular brightness, fluorescence fold, and dark recovery rate. The residues F244 and V276 modulate the maximum absorption and emission peak position. The reverse mutant L168M exhibited a higher fluorescence fold than PAiRFP1. Additionally, the reverse mutants V203A, V294E, S218G and D127G possessed better spectral properties than PAiRFP1. This study is important for the rational design of a better BphP-based photoactivatable NIR-FPs.
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Affiliation(s)
- Faez Iqbal Khan
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China
| | - Honghong Song
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Fakhrul Hassan
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Jing Tian
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Lixia Tang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Dakun Lai
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China.
| | - Feng Juan
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China.
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Bhatt P, Joshi T, Bhatt K, Zhang W, Huang Y, Chen S. Binding interaction of glyphosate with glyphosate oxidoreductase and C-P lyase: Molecular docking and molecular dynamics simulation studies. JOURNAL OF HAZARDOUS MATERIALS 2021; 409:124927. [PMID: 33450511 DOI: 10.1016/j.jhazmat.2020.124927] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 12/14/2020] [Accepted: 12/20/2020] [Indexed: 05/12/2023]
Abstract
Widespread application of glyphosate poses a threat to living organisms. Microbial strains are able to degrade glyphosate via contrasting metabolic pathways with the help of enzymes. Glyphosate oxidoreductase (GOX) and C-P lyase are the key enzymes for the biodegradation of glyphosate and its intermediate metabolite aminomethylphosphonic acid (AMPA) in microbes. The microbial degradation of glyphosate has been reported, but the underlying molecular mechanism is still unclear. Therefore, in this study, the interaction mechanism of GOX and C-P lyase with glyphosate and AMPA were investigated by using molecular docking and molecular dynamics (MD) simulations. The results indicate that glyphosate contacts with the active site of GOX and C-P lyase by hydrogen bonds as well as hydrophobic and van der Waals interactions in aqueous solution to maintain its stability. The presence of glyphosate and AMPA in the active site significantly changes the conformation of GOX and C-P lyase. The results of the MD simulations confirm that GOX and C-P lyase complexes are stable during the catalytic reaction. This study offers a molecular level of understanding of the expression and function of GOX and C-P lyase for the bioremediation of glyphosate.
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Affiliation(s)
- Pankaj Bhatt
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Tushar Joshi
- Department of Biotechnology, Kumaun University, Bhimtal Campus, Bhimtal, Uttarakhand 263136, India
| | - Kalpana Bhatt
- Department of Botany and Microbiology, Gurukul Kangri University, Haridwar, Uttarakhand 249404, India
| | - Wenping Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Yaohua Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Shaohua Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.
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137
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Alves KMA, Cardoso FJB, Honorio KM, de Molfetta FA. Design of Inhibitors for Glyceraldehyde-3-phosphate Dehydrogenase (GAPDH) Enzyme of <i>Leishmania mexicana</i>. Med Chem 2021; 16:784-795. [PMID: 31309897 DOI: 10.2174/1573406415666190712111139] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 06/24/2019] [Accepted: 06/24/2019] [Indexed: 01/04/2023]
Abstract
BACKGROUND Leishmaniosis is a neglected tropical disease and glyceraldehyde 3- phosphate dehydrogenase (GAPDH) is a key enzyme in the design of new drugs to fight this disease. OBJECTIVE The present study aimed to evaluate potential inhibitors of GAPDH enzyme found in Leishmania mexicana (L. mexicana). METHODS A search for novel antileishmanial molecules was carried out based on similarities from the pharmacophoric point of view related to the binding site of the crystallographic enzyme using the ZINCPharmer server. The molecules selected in this screening were subjected to molecular docking and molecular dynamics simulations. RESULTS Consensual analysis of the docking energy values was performed, resulting in the selection of ten compounds. These ligand-receptor complexes were visually inspected in order to analyze the main interactions and subjected to toxicophoric evaluation, culminating in the selection of three compounds, which were subsequently submitted to molecular dynamics simulations. The docking results showed that the selected compounds interacted with GAPDH from L. mexicana, especially by hydrogen bonds with Cys166, Arg249, His194, Thr167, and Thr226. From the results obtained from molecular dynamics, it was observed that one of the loop regions, corresponding to the residues 195-222, can be related to the fitting of the substrate at the binding site, assisting in the positioning and the molecular recognition via residues responsible for the catalytic activity. CONCLUSION The use of molecular modeling techniques enabled the identification of promising compounds as inhibitors of the GAPDH enzyme from L. mexicana, and the results obtained here can serve as a starting point to design new and more effective compounds than those currently available.
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Affiliation(s)
- Krisnna M A Alves
- Laboratorio de Modelagem Molecular, Instituto de Ciencias Exatas e Naturais, Universidade Federal do Para, CP 11101, 60075-110, Belem, PA, Brazil
| | - Fábio José Bonfim Cardoso
- Laboratorio de Modelagem Molecular, Instituto de Ciencias Exatas e Naturais, Universidade Federal do Para, CP 11101, 60075-110, Belem, PA, Brazil
| | - Kathia M Honorio
- Escola de Artes, Ciencias e Humanidades, Universidade de Sao Paulo (USP), 03828-000, Sao Paulo, SP, Brazil.,Universidade Federal do ABC (UFABC), Santo André, SP, Brazil
| | - Fábio A de Molfetta
- Laboratorio de Modelagem Molecular, Instituto de Ciencias Exatas e Naturais, Universidade Federal do Para, CP 11101, 60075-110, Belem, PA, Brazil
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138
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Mwangi HN, Muge EK, Wagacha PW, Ndakala A, Mulaa FJ. Methods for Identifying Microbial Natural Product Compounds that Target Kinetoplastid RNA Structural Motifs by Homology and De Novo Modeled 18S rRNA. Int J Mol Sci 2021; 22:4493. [PMID: 33925823 PMCID: PMC8123475 DOI: 10.3390/ijms22094493] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 02/22/2021] [Accepted: 02/24/2021] [Indexed: 01/16/2023] Open
Abstract
The development of novel anti-infectives against Kinetoplastids pathogens targeting proteins is a big problem occasioned by the antigenic variation in these parasites. This is also a global concern due to the zoonosis of these parasites, as they infect both humans and animals. Therefore, we need not only to create novel antibiotics, but also to speed up the development pipeline for these antibiotics. This may be achieved by using novel drug targets for Kinetoplastids drug discovery. In this study, we focused our attention on motifs of rRNA molecules that have been created using homology modeling. The RNA is the most ambiguous biopolymer in the kinetoplatid, which carries many different functions. For instance, tRNAs, rRNAs, and mRNAs are essential for gene expression both in the pro-and eukaryotes. However, all these types of RNAs have sequences with unique 3D structures that are specific for kinetoplastids only and can be used to shut down essential biochemical processes in kinetoplastids only. All these features make RNA very potent targets for antibacterial drug development. Here, we combine in silico methods combined with both computational biology and structure prediction tools to address our hypothesis. In this study, we outline a systematic approach for identifying kinetoplastid rRNA-ligand interactions and, more specifically, techniques that can be used to identify small molecules that target particular RNA. The high-resolution optimized model structures of these kineoplastids were generated using RNA 123, where all the stereochemical conflicts were solved and energies minimized to attain the best biological qualities. The high-resolution optimized model's structures of these kinetoplastids were generated using RNA 123 where all the stereochemical conflicts were solved and energies minimized to attain the best biological qualities. These models were further analyzed to give their docking assessment reliability. Docking strategies, virtual screening, and fishing approaches successfully recognized novel and myriad macromolecular targets for the myxobacterial natural products with high binding affinities to exploit the unmet therapeutic needs. We demonstrate a sensible exploitation of virtual screening strategies to 18S rRNA using natural products interfaced with classical maximization of their efficacy in phamacognosy strategies that are well established. Integration of these virtual screening strategies in natural products chemistry and biochemistry research will spur the development of potential interventions to these tropical neglected diseases.
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Affiliation(s)
- Harrison Ndung’u Mwangi
- Department of Biochemistry, University of Nairobi, Nairobi 00200-30197, Kenya; (E.K.M.); (F.J.M.)
| | - Edward Kirwa Muge
- Department of Biochemistry, University of Nairobi, Nairobi 00200-30197, Kenya; (E.K.M.); (F.J.M.)
| | - Peter Waiganjo Wagacha
- Department of Computing and Informatics, University of Nairobi, Nairobi 00200-30197, Kenya;
| | - Albert Ndakala
- Department of Chemistry, University of Nairobi, Nairobi 00200-30197, Kenya;
| | - Francis Jackim Mulaa
- Department of Biochemistry, University of Nairobi, Nairobi 00200-30197, Kenya; (E.K.M.); (F.J.M.)
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139
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Tahir Ul Qamar M, Ahmad S, Fatima I, Ahmad F, Shahid F, Naz A, Abbasi SW, Khan A, Mirza MU, Ashfaq UA, Chen LL. Designing multi-epitope vaccine against Staphylococcus aureus by employing subtractive proteomics, reverse vaccinology and immuno-informatics approaches. Comput Biol Med 2021; 132:104389. [PMID: 33866250 DOI: 10.1016/j.compbiomed.2021.104389] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/27/2021] [Accepted: 04/07/2021] [Indexed: 01/28/2023]
Abstract
Staphylococcus aureus is a deadly human bacterial pathogen that causes a wide variety of clinical manifestations. Invasive S. aureus infections in hospitals and the community are one of the main causes of mortality and morbidity, as virulent and multi-drug-resistant strains have evolved. There is an unmet and urgent clinical need for immune-based non-antibiotic approaches to treat these infections as the growing antibiotic resistance poses a significant public health danger. Subtractive proteomics assisted reverse vaccinology-based immunoinformatics pipeline was used in this study to target the suitable antigenic proteins for the development of multi-epitope vaccine (MEV). Three essential virulent and antigenic proteins were identified including Glycosyltransferase, Elastin Binding Protein, and Staphylococcal secretory antigen. A variety of immunoinformatics tools have been used to forecast T-cell and B-cell epitopes from target proteins. Seven CTL, five HTL, and eight LBL epitopes, connected through suitable linkers and adjuvant, were employed to design 444 amino acids long MEV construct. The vaccine was paired with the TLR4 agonist 50S ribosomal protein L7/L12 adjuvant to enhance the immune response towards the vaccine. The predicted MEV structure was assessed to be highly antigenic, non-toxic, non-allergenic, flexible, stable, and soluble. Molecular docking simulation of the MEV with the human TLR4 (toll-like receptor 4) and major histocompatibility complex molecules (MHCI and MHCII) was performed to validate the interactions with the receptors. Molecular dynamics (MD) simulation and MMGBSA binding free energy analyses were carried out for the stability evaluation and binding of the MEV docked complexes with TLR4, MHCI and MHCII. To achieve maximal vaccine protein expression with optimal post-translational modifications, MEV was reverse translated, its mRNA structure was analyzed, and finally in silico cloning was performed into E. coli expression host. These rigorous computational analyses supported the effectivity of proposed MEV in protection against infections associated with S. aureus. However, further experimental validations are required to fully evaluate the potential of proposed vaccine candidate.
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Affiliation(s)
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
| | - Israr Fatima
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Faisal Ahmad
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Farah Shahid
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Anam Naz
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Sumra Wajid Abbasi
- NUMS Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Muhammad Usman Mirza
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Canada
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Ling-Ling Chen
- College of Life Science and Technology, Guangxi University, Nanning, PR China.
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140
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Sultan A, Ali R, Sultan T, Ali S, Khan NJ, Parganiha A. Circadian clock modulating small molecules repurposing as inhibitors of SARS-CoV-2 M pro for pharmacological interventions in COVID-19 pandemic. Chronobiol Int 2021; 38:971-985. [PMID: 33820462 PMCID: PMC8022342 DOI: 10.1080/07420528.2021.1903027] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 is a global health emergency warranting the development of targeted treatment. The main protease Mpro is considered as a key drug target in coronavirus infections because of its vital role in the proteolytic processing of two essential polyproteins required for the replication and transcription of viral RNA. Targeting and inhibiting the Mpro activity represents a valid approach to prevent the SARS-CoV-2 replication and spread. Based on the structure-assisted drug designing, here we report a circadian clock-modulating small molecule “SRT2183” as a potent inhibitor of Mpro to block the replication of SARS-CoV-2. The findings are expected to pave the way for the development of therapeutics for COVID-19.
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Affiliation(s)
- Armiya Sultan
- Functional Genomics Laboratory, Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia (A Central University), New Delhi, India.,Department of Biosciences, Jamia Millia Islamia (A Central University), New Delhi, India.,Chronobiology and Animal Behaviour Laboratory, School of Studies in Life Sciences, Pt. Ravishankar Shukla University, Raipur, India
| | - Rafat Ali
- Department of Biosciences, Jamia Millia Islamia (A Central University), New Delhi, India
| | - Tahira Sultan
- Department of Biochemistry, University of Kashmir, Srinagar, India
| | - Sher Ali
- Department of Life Sciences, Sharda University, Greater Noida, India
| | - Nida Jamil Khan
- Department of Biosciences, Jamia Millia Islamia (A Central University), New Delhi, India
| | - Arti Parganiha
- Chronobiology and Animal Behaviour Laboratory, School of Studies in Life Sciences, Pt. Ravishankar Shukla University, Raipur, India
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141
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Zia MK, Siddiqui T, Ahsan H, Khan FH. Characterization of the binding between anti-tumor drug 5-fluorouracil and human alpha-2-macroglobulin: spectroscopic and molecular docking analyses. J Biomol Struct Dyn 2021; 40:7949-7959. [PMID: 33798029 DOI: 10.1080/07391102.2021.1905550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
5-Fluorouracil (5-FU) is a well-recognized anticancer drug used in the treatment of tumors of head, neck and breast. Drug pharmacokinetics is affected upon binding with protein, thus, making drug-protein interactions imperative to study. Present work investigates the interaction between 5-FU and human major antiproteinase-alpha-2-macroglobulin (α2M) by multi-spectroscopic, calorimetric and molecular docking techniques. UV/Visible absorption, intrinsic fluorescence and circular dichroism (CD) spectroscopic methods have been employed to unveil the mode and mechanism of 5-FU-α2M interaction. Synchronous fluorescence showed alteration in the microenvironment of tryptophan and tyrosine residues of protein. Far UV-CD spectra suggest slight alterations in the secondary structure of α2M by 5-FU. Thermodynamic parameters determined by fluorescence quenching experiments and isothermal titration calorimetry (ITC) suggested the involvement of hydrogen bonds and hydrophobic interactions. Moreover, ITC corroborate the spontaneous and exothermic nature of the interaction process. Molecular docking illustrates that 5-FU binds with moderate affinity and Asp953, Tyr1264, Lys1236, Thr1232, Tyr1323 and Leu951 were the main residues involved. Molecular dynamics simulation studies suggested that 5-FU was stabilizing the α2M structure and forming a stable complex. It was concluded that 5-FU lower the antiproteolytic activity of α2M significantly and causes disruption in the native structure and conformation of α2M.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohammad Khalid Zia
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
| | - Tooba Siddiqui
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
| | - Haseeb Ahsan
- Department of Biochemistry, Faculty of Dentistry, Jamia Millia Islamia, New Delhi, India
| | - Fahim Halim Khan
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
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142
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Jairajpuri DS, Hussain A, Nasreen K, Mohammad T, Anjum F, Tabish Rehman M, Mustafa Hasan G, Alajmi MF, Imtaiyaz Hassan M. Identification of natural compounds as potent inhibitors of SARS-CoV-2 main protease using combined docking and molecular dynamics simulations. Saudi J Biol Sci 2021; 28:2423-2431. [PMID: 33526965 PMCID: PMC7839507 DOI: 10.1016/j.sjbs.2021.01.040] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/17/2021] [Accepted: 01/19/2021] [Indexed: 12/12/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) has emerged from China and globally affected the entire population through the human-to-human transmission of a newly emerged virus called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The genome of SARS-CoV-2 encodes several proteins that are essential for multiplication and pathogenesis. The main protease (Mpro or 3CLpro) of SARS-CoV-2 plays a central role in its pathogenesis and thus is considered as an attractive drug target for the drug design and development of small-molecule inhibitors. We have employed an extensive structure-based high-throughput virtual screening to discover potential natural compounds from the ZINC database which could inhibit the Mpro of SARS-CoV-2. Initially, the hits were selected on the basis of their physicochemical and drug-like properties. Subsequently, the PAINS filter, estimation of binding affinities using molecular docking, and interaction analyses were performed to find safe and potential inhibitors of SARS-CoV-2 Mpro. We have identified ZINC02123811 (1-(3-(2,5,9-trimethyl-7-oxo-3-phenyl-7H-furo[3,2-g]chromen-6-yl)propanoyl)piperidine-4-carboxamide), a natural compound bearing appreciable affinity, efficiency, and specificity towards the binding pocket of SARS-CoV-2 Mpro. The identified compound showed a set of drug-like properties and preferentially binds to the active site of SARS-CoV-2 Mpro. All-atom molecular dynamics (MD) simulations were performed to evaluate the conformational dynamics, stability and interaction mechanism of Mpro with ZINC02123811. MD simulation results indicated that Mpro with ZINC02123811 forms a stable complex throughout the trajectory of 100 ns. These findings suggest that ZINC02123811 may be further exploited as a promising scaffold for the development of potential inhibitors of SARS-CoV-2 Mpro to address COVID-19.
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Affiliation(s)
- Deeba Shamim Jairajpuri
- Department of Medical Biochemistry, College of Medicine and Medical Sciences, Arabian Gulf University, P.O. Box 22971, Manama, Bahrain
| | - Afzal Hussain
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Khalida Nasreen
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Farah Anjum
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Md. Tabish Rehman
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Gulam Mustafa Hasan
- Department of Biochemistry, College of Medicine, Prince Sattam Bin Abdulaziz University, P.O. Box 173 Al-Kharj, 11942, Saudi Arabia
| | - Mohamed F. Alajmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Md. Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
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Small Molecule "Silmitasertib" Repurposed as Inhibitor of Transforming Growth Factor Beta 1 for the Development of Therapeutics for Oral Submucous Fibrosis. BIOMED RESEARCH INTERNATIONAL 2021; 2021:6631848. [PMID: 33869629 PMCID: PMC8035005 DOI: 10.1155/2021/6631848] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/12/2021] [Accepted: 03/19/2021] [Indexed: 11/17/2022]
Abstract
Oral submucous fibrosis (OSMF) is considered a premalignant condition characterized by aggressive fibrosis of the submucosal tissues of the oral cavity reflecting its malignant transformation potential. Activation of transforming growth factor beta (TGF-β) signaling has been reported to lead increased collagen production and fibrosis. Recently, significant upregulation of TGF-β1 has been reported in OSMF as compared to normal tissues. Therefore, inhibition of the TGF-β1 may pave for the development of therapeutics of OSMF. Based on the structure-assisted drug designing, we found "silmitasertib" as potent inhibitor of TGF-β1. We suggest that this molecule can be validated and implemented for the treatment of OSMF.
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144
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Hafidi Z, El Achouri M, O Sousa FF, Pérez L. Antifungal activity of amino-alcohols based cationic surfactants and in silico, homology modeling, docking and molecular dynamics studies against lanosterol 14-α-demethylase enzyme. J Biomol Struct Dyn 2021; 40:7762-7778. [PMID: 33754947 DOI: 10.1080/07391102.2021.1902396] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Fungi are being responsible for causing serious infections in humans and animals. The opportunistic microorganisms provoke environmental contaminations in health and storage facilities to represent a serious concern to health security. The present work investigates the antifungal activity of two amino-alcohols based cationic surfactants such as CnEtOH, CnPrOH (with n = 14 and 16 are the carbon numbers of alkyl chain and EtOH = Ethanol and PrOH = Propanol) against a collection of different Candida species (Candida tropicalis, Candida albicans, Candida auris, Cyberlindnera jadinii, Candida parapsilosis, Candida glabrata and Candida rugosa) respectively. The amino-alcohols based cationic surfactants exhibited good antifungal activity against all Candida strains tested with minimum inhibitory concentrations (MIC) ranging from 0.002 to 0.30 mM. The MIC evaluation shows an increase as a function of the hydrophobicity of all inhibitors against the majority of the Candida strains tested. The different location of the alcoholic OH function in the polar head shows the influence on the availability of N+ responsible for electrostatic interactions with the candidate's cell walls, which remains a very important step in the mode of action of quaternary ammonium cationic surfactants. Hence, a 3D structure of lanosterol 14-α-demethylase enzyme from C. auris was constructed by homology modeling using an online SWISS-MODEL server. The predicted model was analyzed by serval servers. Furthermore, a molecular docking study was carried out to better understand the binding mechanism of lanosterol homologous protein with surfactant ligands. Then, the docked complexes lanosterol-surfactants were refined by the molecular dynamic simulation to analyze their interaction behavior during the simulation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Zakaria Hafidi
- Laboratoire de Physico-Chimie des Matériaux Inorganiques et Organiques, Ecole Normale supérieure-Rabat, Mohammed V University in Rabat, Centre des Sciences des Matériaux, Rabat, Morocco.,Surfactants and Nanobiotechnology Department, IQAC, CSIC, Barcelona, Spain
| | - Mohammed El Achouri
- Laboratoire de Physico-Chimie des Matériaux Inorganiques et Organiques, Ecole Normale supérieure-Rabat, Mohammed V University in Rabat, Centre des Sciences des Matériaux, Rabat, Morocco
| | - Francisco F O Sousa
- Surfactants and Nanobiotechnology Department, IQAC, CSIC, Barcelona, Spain.,Graduate Program on Pharmaceutical Innovation, Department of Biological & Health Sciences, Federal University of Amapa, Rodovia Juscelino Kubitschek, Macapa, Amapá, Brazil
| | - Lourdes Pérez
- Surfactants and Nanobiotechnology Department, IQAC, CSIC, Barcelona, Spain
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145
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Hachim ME, Oubella A, Byadi S, Fawzi M, Laamari Y, Bahsis L, Aboulmouhajir A, Morjani H, Podlipnik Č, Auhmani A, Ait Itto MY. Newly synthesized (R)-carvone-derived 1,2,3-triazoles: structural, mechanistic, cytotoxic and molecular docking studies. J Biomol Struct Dyn 2021; 40:7205-7217. [DOI: 10.1080/07391102.2021.1894984] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Mouhi Eddine Hachim
- Équipe de modélisation moléculaire et de spectroscopie, Faculté des sciences, Université de Chouaïb Doukkali, El Jadida, Morocco
| | - Ali Oubella
- Département de Chimie, Faculté desSciences, Laboratoire de Synthèse Organique et Physico-Chimie Moléculaire, Marrakech, Morocco
| | - Said Byadi
- Équipe de spectroscopie d'extraction et de valorisation, Synthèse organique, Laboratoire d'extraction et de valorisation, Faculté des sciences d'Ain Chock, Université Hassan II, Casablanca, Morocco
| | - Mourad Fawzi
- Département de Chimie, Faculté desSciences, Laboratoire de Synthèse Organique et Physico-Chimie Moléculaire, Marrakech, Morocco
| | - Yassine Laamari
- Département de Chimie, Faculté desSciences, Laboratoire de Synthèse Organique et Physico-Chimie Moléculaire, Marrakech, Morocco
| | - Lahoucine Bahsis
- Laboratoire de Chimie de Coordination et d'Analytique, Département de Chimie, Faculté des Sciences d’El Jadida, Université Chouaïb Doukkali, El Jadida, Morocco
| | - Aziz Aboulmouhajir
- Équipe de modélisation moléculaire et de spectroscopie, Faculté des sciences, Université de Chouaïb Doukkali, El Jadida, Morocco
- Équipe de spectroscopie d'extraction et de valorisation, Synthèse organique, Laboratoire d'extraction et de valorisation, Faculté des sciences d'Ain Chock, Université Hassan II, Casablanca, Morocco
| | - Hamid Morjani
- BioSpectroscopie Translationnelle, BioSpecT - EA7506, UFR de Pharmacie, Université de Reims Champagne-Ardenne, Reims Cedex, France
| | - Črtomir Podlipnik
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Aziz Auhmani
- Département de Chimie, Faculté desSciences, Laboratoire de Synthèse Organique et Physico-Chimie Moléculaire, Marrakech, Morocco
| | - My Youssef Ait Itto
- Département de Chimie, Faculté desSciences, Laboratoire de Synthèse Organique et Physico-Chimie Moléculaire, Marrakech, Morocco
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Omolabi KF, Agoni C, Olotu FA, Soliman ME. ‘Finding the needle in the haystack’- will natural products fit for purpose in the treatment of cryptosporidiosis? – A theoretical perspective. MOLECULAR SIMULATION 2021. [DOI: 10.1080/08927022.2021.1895435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Kehinde F. Omolabi
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Clement Agoni
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Fisayo A. Olotu
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Mahmoud E.S. Soliman
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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147
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Pereira GRC, Vieira BDAA, De Mesquita JF. Comprehensive in silico analysis and molecular dynamics of the superoxide dismutase 1 (SOD1) variants related to amyotrophic lateral sclerosis. PLoS One 2021; 16:e0247841. [PMID: 33630959 PMCID: PMC7906464 DOI: 10.1371/journal.pone.0247841] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 02/15/2021] [Indexed: 12/29/2022] Open
Abstract
Amyotrophic Lateral Sclerosis (ALS) is the most frequent motor neuron disorder, with a significant social and economic burden. ALS remains incurable, and the only drugs approved for its treatments confers a survival benefit of a few months for the patients. Missense mutations in superoxide dismutase 1 (SOD1), a major cytoplasmic antioxidant enzyme, has been associated with ALS development, accounting for 23% of its familial cases and 7% of all sporadic cases. This work aims to characterize in silico the structural and functional effects of SOD1 protein variants. Missense mutations in SOD1 were compiled from the literature and databases. Twelve algorithms were used to predict the functional and stability effects of these mutations. ConSurf was used to estimate the evolutionary conservation of SOD1 amino-acids. GROMACS was used to perform molecular dynamics (MD) simulations of SOD1 wild-type and variants A4V, D90A, H46R, and I113T, which account for approximately half of all ALS-SOD1 cases in the United States, Europe, Japan, and United Kingdom, respectively. 233 missense mutations in SOD1 protein were compiled from the databases and literature consulted. The predictive analyses pointed to an elevated rate of deleterious and destabilizing predictions for the analyzed variants, indicating their harmful effects. The ConSurf analysis suggested that mutations in SOD1 mainly affect conserved and possibly functionally essential amino acids. The MD analyses pointed to flexibility and essential dynamics alterations at the electrostatic and metal-binding loops of variants A4V, D90A, H46R, and I113T that could lead to aberrant interactions triggering toxic protein aggregation. These alterations may have harmful implications for SOD1 and explain their association with ALS. Understanding the effects of SOD1 mutations on protein structure and function facilitates the design of further experiments and provides relevant information on the molecular mechanism of pathology, which may contribute to improvements in existing treatments for ALS.
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Affiliation(s)
- Gabriel Rodrigues Coutinho Pereira
- Department of Genetics and Molecular Biology, Bioinformatics and Computational Biology Laboratory, Federal University of the State of Rio de Janeiro (UNIRIO), Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Joelma Freire De Mesquita
- Department of Genetics and Molecular Biology, Bioinformatics and Computational Biology Laboratory, Federal University of the State of Rio de Janeiro (UNIRIO), Rio de Janeiro, Rio de Janeiro, Brazil
- * E-mail:
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148
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Khan S, Shaker B, Ahmad S, Abbasi SW, Arshad M, Haleem A, Ismail S, Zaib A, Sajjad W. Towards a novel peptide vaccine for Middle East respiratory syndrome coronavirus and its possible use against pandemic COVID-19. J Mol Liq 2021; 324:114706. [PMID: 33173250 PMCID: PMC7644433 DOI: 10.1016/j.molliq.2020.114706] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 09/05/2020] [Accepted: 11/02/2020] [Indexed: 12/02/2022]
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) is an emerging health concern due to its high mortality rate of 35%. At present, no vaccine is available to protect against MERS-CoV infections. Therefore, an in silico search for potential antigenic epitopes in the non-redundant proteome of MERS-CoV was performed herein. First, a subtractive proteome-based approach was employed to look for the surface exposed and host non-homologous proteins. Following, immunoinformatics analysis was performed to predict antigenic B and T cell epitopes that were used in the design of a multi-epitopes peptide. Molecular docking study was carried out to predict vaccine construct affinity of binding to Toll-like receptor 3 (TLR3) and understand its binding conformation to extract ideas about its processing by the host immune system. We identified membrane protein, envelope small membrane protein, non-structural protein ORF3, non-structural protein ORF5, and spike glycoprotein as potential candidates for subunit vaccine designing. The designed multi-epitope peptide then linked to β-defensin adjuvant is showing high antigenicity. Further, the sequence of the designed vaccine construct is optimized for maximum expression in the Escherichia coli expression system. A rich pattern of hydrogen and hydrophobic interactions of the construct was observed with the TLR3 allowing stable binding of the construct at the docked site as predicted by the molecular dynamics simulation and MM-PBSA binding energies. We expect that the panel of subunit vaccine candidates and the designed vaccine construct could be highly effective in immunizing populations from infections caused by MERS-CoV and could possible applied on the current pandemic COVID-19.
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Affiliation(s)
- Salman Khan
- School of Life Sciences, Lanzhou University, Lanzhou, Gansu 73000, PR China
| | - Bilal Shaker
- School of Integrative Engineering, Chung ANG University, Seoul, South Korea
| | - Sajjad Ahmad
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Sumra Wajid Abbasi
- Department of Biological Sciences, National University of Medical Sciences, the Mall, Rawalpindi 46000, Pakistan
| | - Muhammad Arshad
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Abdul Haleem
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Saba Ismail
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Anita Zaib
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Wasim Sajjad
- Department of Biological Sciences, National University of Medical Sciences, the Mall, Rawalpindi 46000, Pakistan
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149
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Wakchaure PD, Ganguly B. Molecular level insights into the inhibition of gene expression by thiamine pyrophosphate (TPP) analogs for TPP riboswitch: A well-tempered metadynamics simulations study. J Mol Graph Model 2021; 104:107849. [PMID: 33545607 DOI: 10.1016/j.jmgm.2021.107849] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 11/30/2020] [Accepted: 01/19/2021] [Indexed: 10/22/2022]
Abstract
Riboswitches are metabolite sensing aptamer domains present in non-coding regions in RNA and act as gene-regulating elements. Thiamine pyrophosphate (TPP) riboswitch is evolved as a new target for developing antibiotics against many pathogenic bacteria. The earlier reports suggest that the modification of the pyrophosphate group in the ligand molecule can enhance gene expression. In this work, we have examined the binding affinity and efficacy of TPP and two recently reported ligands, CH2-TPP, and CF2-TPP, using Well-tempered metadynamics (WT-MtD) simulations. The experimental in vitro assays show that both TPP and CH2-TPP repress the gene expression to the same extent. The calculated binding energies correlate well with the experimental study and show the same trend of binding affinity of ligands for the TPP riboswitch. The root mean square fluctuation profiles suggest that the CH2-TPP and TPP trigger higher fluctuations in P1 and L3 region, and such fluctuations in the P1 region is involved in the gene regulation process. The metal ion mediated contact of TPP ligand with pyrophosphate binding helix is found to be critical in the gene regulation process. The simulation results corroborate the experimental observations that the role of conformational changes occurring in different riboswitch regions upon ligand binding is essential to repress the gene expression process. This work sheds light on the subtle change in the ligand structure that can induce a more considerable impact on binding affinity and efficacy of ligands with riboswitch.
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Affiliation(s)
- Padmaja D Wakchaure
- Computation and Simulation Unit (Analytical Discipline and Centralized Instrument Facility), CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, 364002, Gujarat, India; Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, 201 002, India
| | - Bishwajit Ganguly
- Computation and Simulation Unit (Analytical Discipline and Centralized Instrument Facility), CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, 364002, Gujarat, India; Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, 201 002, India.
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150
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Biocomputational Prediction Approach Targeting FimH by Natural SGLT2 Inhibitors: A Possible Way to Overcome the Uropathogenic Effect of SGLT2 Inhibitor Drugs. Molecules 2021; 26:molecules26030582. [PMID: 33499241 PMCID: PMC7866138 DOI: 10.3390/molecules26030582] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/16/2021] [Accepted: 01/19/2021] [Indexed: 01/05/2023] Open
Abstract
The Food and Drug Administration (FDA) approved a new class of anti-diabetic medication (a sodium-glucose co-transporter 2 (SGLT2) inhibitor) in 2013. However, SGLT2 inhibitor drugs are under evaluation due to their associative side effects, such as urinary tract and genital infection, urinary discomfort, diabetic ketosis, and kidney problems. Even clinicians have difficulty in recommending it to diabetic patients due to the increased probability of urinary tract infection. In our study, we selected natural SGLT2 inhibitors, namely acerogenin B, formononetin, (-)-kurarinone, (+)-pteryxin, and quinidine, to explore their potential against an emerging uropathogenic bacterial therapeutic target, i.e., FimH. FimH plays a critical role in the colonization of uropathogenic bacteria on the urinary tract surface. Thus, FimH antagonists show promising effects against uropathogenic bacterial strains via their targeting of FimH's adherence mechanism with less chance of resistance. The molecular docking results showed that, among natural SGLT2 inhibitors, formononetin, (+)-pteryxin, and quinidine have a strong interaction with FimH proteins, with binding energy (∆G) and inhibition constant (ki) values of -5.65 kcal/mol and 71.95 µM, -5.50 kcal/mol and 92.97 µM, and -5.70 kcal/mol and 66.40 µM, respectively. These interactions were better than those of the positive control heptyl α-d-mannopyranoside and far better than those of the SGLT2 inhibitor drug canagliflozin. Furthermore, a 50 ns molecular dynamics simulation was conducted to optimize the interaction, and the resulting complexes were found to be stable. Physicochemical property assessments predicted little toxicity and good drug-likeness properties for these three compounds. Therefore, formononetin, (+)-pteryxin, and quinidine can be proposed as promising SGLT2 inhibitors drugs, with add-on FimH inhibition potential that might reduce the probability of uropathogenic side effects.
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