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Alkholifi FK, Abdi SAH, Qadri M, Sayed SF, Khardali A, Nagarajan S, Abdulrahman A, Aldabaan N, Alghazwani Y. Hexaconazole exposure may lead to Parkinson via disrupting glucocerebrosidase and parkin: molecular interaction, dynamics, MMPBSA and DFT based in-silico predictive toxicology. Toxicol Res (Camb) 2024; 13:tfae018. [PMID: 38496321 PMCID: PMC10939372 DOI: 10.1093/toxres/tfae018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/05/2024] [Accepted: 01/16/2024] [Indexed: 03/19/2024] Open
Abstract
Hexaconazole is a known fungicide for agricultural purposes. It has bioaccumulation ability which makes it important for its toxicological characterization. There are various neurological impacts of pollutants on human health. Therefore, in this study, we have done predictive analyses of the interaction mechanism of hexaconazole by molecular interaction analysis, molecular dynamics simulation, and Poisson-Boltzmann surface area (MM-PBSA) to assess hexaconazole's potency to disrupt the homeostasis of glucocerebrosidase (-7.9 kcal/mol) and parkin (-5.67 kcal/mol) proteins which have significant roles in the manifestation of Parkinson disease. The findings reveal that hexaconazole has the potency to form stable interactions with glucocerebrosidase and parkin. This research provides a molecular and atomic-level understanding of how hexaconazole exposure may disrupt the homeostasis of glucocerebrosidase and parkin. The root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration, and hydrogen bonding exhibited the potent molecular interactions of hexaconazole, which may lead to neurological manifestations such as Parkinson disease.
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Affiliation(s)
- Faisal K Alkholifi
- Department of Pharmacology, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Abdullah bin Amer Street, Riyadh region, Al-Kharj 16278, Saudi Arabia
| | - Sayed Aliul Hasan Abdi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Al-Baha University, Al-Baha 65779, Saudi Arabia
| | - Marwa Qadri
- Department of Pharmacology and Toxicology, College of Pharmacy, Jazan University, Jazan 45142, Saudi Arabia
- Inflammation Pharmacology and Drug Discovery Unit, Health Science Research Center (HSRC), Jazan University, Jazan 45142, Saudi Arabia
| | - Shabihul Fatma Sayed
- Department of Nursing, Farasan University College, Jazan University, 54943, Saudi Arabia
| | - Amani Khardali
- Department of Clinical Pharmacy, College of Pharmacy, Jazan University, Jazan 45142 Saudi Arabia
- Pharmacy Practice Research Unit, College of Pharmacy, Jazan University, Jazan, 45142, Saudi Arabia
| | - Sumathi Nagarajan
- Department of Nursing, Farasan University College, Jazan University, 54943, Saudi Arabia
| | - Alhamyani Abdulrahman
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Al-Baha University, Al-Baha 65779, Saudi Arabia
| | - Nayef Aldabaan
- Department of Pharmacology, College of Pharmacy, Najran University, Najran 61441, Saudi Arabia
| | - Yahia Alghazwani
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha 61421, Saudi Arabia
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Alquraini A. Potency of Hexaconazole to Disrupt Endocrine Function with Sex Hormone-Binding Globulin. Int J Mol Sci 2023; 24:ijms24043882. [PMID: 36835294 PMCID: PMC9964258 DOI: 10.3390/ijms24043882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 01/27/2023] [Accepted: 02/06/2023] [Indexed: 02/17/2023] Open
Abstract
Hexaconazole is widely used as a fungicide for agricultural purposes. However, the endocrine-disrupting potential of hexaconazole is still under investigation. In addition, an experimental study found that hexaconazole may disrupt the normal synthesis of steroidal hormones. The potency of hexaconazole to bind with sex hormone-binding globulin (SHBG), a plasma carrier protein that binds androgens and oestrogens, is unknown. In this study, we evaluated the efficacy of hexaconazole to bind with SHBG by molecular interaction, a molecular dynamics method. In addition, principal component analysis was performed to understand the dynamical behaviour of hexaconazole with SHBG in comparison with dihydrotestosterone and aminoglutethimide. The binding scores of hexaconazole, dihydrotestosterone, and aminoglutethimide with SHBG were found to be -7.12 kcal/mol, -11.41 kcal/mol, and -6.84 kcal/mol, respectively. With respect to stable molecular interaction, hexaconazole showed similar molecular dynamics patterns of root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), and hydrogen bonding. The solvent surface area (SASA) and principal component analysis (PCA) of hexaconazole exhibit similar patterns in comparison with dihydrotestosterone and aminoglutethimide. These results show that hexaconazole has a stable molecular interaction with SHBG, which may acquire the active site of the native ligand, resulting in significant endocrine disruption during agricultural work.
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Affiliation(s)
- Ali Alquraini
- Department of Pharmaceutical Chemistry, Faculty of Clinical Pharmacy, Al Baha University, Al Baha 65779, Saudi Arabia
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Sunscreen Ingredient Octocrylene's Potency to Disrupt Vitamin D Synthesis. Int J Mol Sci 2022; 23:ijms231710154. [PMID: 36077552 PMCID: PMC9456232 DOI: 10.3390/ijms231710154] [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: 07/30/2022] [Revised: 08/28/2022] [Accepted: 08/30/2022] [Indexed: 11/17/2022] Open
Abstract
Octocrylene is a widely used ingredient in sunscreen products, and it has been observed that the use of sunscreen has been increasing over the last few decades. In this paper, we investigated the way in which sunscreen's ingredient octocrylene may disrupt normal vitamin D synthesis pathway, resulting in an imbalance in vitamin D levels in the body. The key techniques used for this insilico investigation were molecular docking, molecular dynamic (MD) simulation, and MMPBSA-based assessment. Vitamin D abnormalities have become very common in human health. Unknown exposure to chemicals may be one of the important risk factors. In molecular docking analysis, octocrylene exhibited a binding energy of -11.52 kcal/mol with vitamin D binding protein (1KXP) and -11.71 for the calcitriol native ligand. Octocrylene had a binding potency of -11.152 kcal/mol with the vitamin D receptor (1DB1), and calcitriol had a binding potency of -8.73 kcal/mol. In addition, octocrylene has shown binding energy of -8.96 kcal/mol with CYP2R1, and the calcitriol binding energy was -10.36 kcal/mol. Regarding stability, the root-mean-square deviation (RMSD), the root-mean-square fluctuation (RMSF), the radius of gyration, hydrogen bonding, and the solvent-accessible surface area (SASA) exhibited that octocrylene has a stable binding pattern similar to calcitriol. These findings revealed that incessant exposure to octocrylene may disrupt normal vitamin D synthesis.
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Iqbal M, Moin ST. Dynamics of metal binding and mutation in yybP-ykoY riboswitch of Lactococcus lactis. RSC Adv 2022; 12:17337-17349. [PMID: 35765457 PMCID: PMC9190785 DOI: 10.1039/d2ra02189g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/30/2022] [Indexed: 11/21/2022] Open
Abstract
Riboswitch is a regulatory segment of messenger RNA (mRNA), which by binding to various cellular metabolites regulates the activity of mRNA via modulating transcription, translation, alternative splicing, and stability of the mRNA. yybP–ykoY riboswitch of Lactococcus lactis, which is present upstream of the yoaB gene, functions as a Mn2+-specific genetic ON-switch, and modulates expression of proteins which are significant for Mn2+ homeostasis. The P1.1 switch helix of the aptamer domain of the riboswitch contains an intrinsic transcription terminator structure, which gets stabilized with Mn2+ binding and causes disruption of terminator structure and allows the continuation of transcription. The current research work involved the evaluation of structural and dynamical properties of the yybP-ykoY riboswitch of L. lactis in its Mn2+-free, Mn2+-bound (wild-type), and Mn2+-bound mutant (A41U) states by applying molecular dynamics simulations. Based on the simulations, the effects of Mn2+ absence and A41U mutation were evaluated on the structure and dynamics of the riboswitches followed by the computation of the free energy of metal binding in the wild-type and the mutant riboswitches. The simulation results provided insights into the properties of the riboswitch with the focus on the dynamics of the P1.1 switch helix, and the manganese binding site designated as MB site, as well as the relative stability of the wild-type and the mutant riboswitches, which helped to understand the structural and dynamical role of the metal ion involved in the function of Mn2+-sensing riboswitch. The current research work involved the evaluation of structural and dynamical properties of yybP–ykoY riboswitch of L. lactis in Mn2+-free, Mn2+-bound (wild-type), and Mn2+-bound mutant (A41U) states by applying molecular dynamics simulations.![]()
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Affiliation(s)
- Mazhar Iqbal
- Third World Center for Science and Technology, H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi Karachi-75270 Pakistan +92-21-348-19018 +92-21-99261774
| | - Syed Tarique Moin
- Third World Center for Science and Technology, H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi Karachi-75270 Pakistan +92-21-348-19018 +92-21-99261774
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Sadeghi M, Miroliaei M, Fateminasab F, Moradi M. Screening cyclooxygenase-2 inhibitors from Allium sativum L. compounds: in silico approach. J Mol Model 2021; 28:24. [PMID: 34970708 DOI: 10.1007/s00894-021-05016-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 12/23/2021] [Indexed: 12/31/2022]
Abstract
Inflammation is a natural protective response toward various simulators, including tissue damage or pathogens. The cyclooxygenase-2 (COX-2) is a very important protein in triggering pain and inflammation. Previous studies have claimed that Allium sativum offers a wide range of anti-inflammatory therapeutics for human consumption. Drug discovery is a complicated process, though in silico methods can make this procedure simpler and more cost-effective. At the current study, we performed the virtual screening of eight Allium sativum-derived compounds via molecular docking with COX-2 enzyme and confirmed the binding energy by docking score estimate followed by ADMET and drug-likeness investigation. The resulting highest-docking scored compound was exposed to molecular dynamics simulation (MDS) for evaluating stability of the docked enzyme-ligand complex and to gauge the oscillation and conformational alterations for the time of enzyme-ligand interaction. The factors of RMSD, RMSF, hydrogen bond interactions, and Rg after 100 ns of MDS proved the stability of alliin in the active site of COX-2 in comparison with celecoxib (CEL) as the control. Moreover, we investigated the binding affinity analysis of all compounds via MM/PBSA method. The results from this study suggest that alliin (a sulfuric compound) exhibits a higher binding affinity for the COX-2 enzyme compared to the other compounds and CEL. Alliin showed to be a possible anti-inflammatory therapeutic candidate for managing the inflammatory conditions.
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Affiliation(s)
- Morteza Sadeghi
- Faculty of Biological Science and Technology, Department of Cell and Molecular Biology & Microbiology, University of Isfahan, Isfahan, Iran
| | - Mehran Miroliaei
- Faculty of Biological Science and Technology, Department of Cell and Molecular Biology & Microbiology, University of Isfahan, Isfahan, Iran.
| | | | - Mohammad Moradi
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
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Golyshev VM, Pyshnyi DV, Lomzov AA. Calculation of Energy for RNA/RNA and DNA/RNA Duplex Formation by Molecular Dynamics Simulation. Mol Biol 2021. [DOI: 10.1134/s002689332105006x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Abstract
The development of approaches for predictive calculation of hybridization properties of various nucleic acid (NA) derivatives is the basis for the rational design of the NA-based constructs. Modern advances in computer modeling methods provide the feasibility of these calculations. We have analyzed the possibility of calculating the energy of DNA/RNA and RNA/RNA duplex formation using representative sets of complexes (65 and 75 complexes, respectively). We used the classical molecular dynamics (MD) method, the MMPBSA or MMGBSA approaches to calculate the enthalpy (ΔH°) component, and the quasi-harmonic approximation (Q-Harm) or the normal mode analysis (NMA) methods to calculate the entropy (ΔS°) contribution to the Gibbs energy ($$\Delta G_{{37}}^{^\circ }$$ ) of the NA complex formation. We have found that the MMGBSA method in the analysis of the MD trajectory of only the NA duplex and the empirical linear approximation allow calculation of the enthalpy of formation of the DNA, RNA, and hybrid duplexes of various lengths and GC content with an accuracy of 8.6%. Within each type of complex, the combination of rather efficient MMGBSA and Q-Harm approaches being applied to the trajectory of only the bimolecular complex makes it possible to calculate the $$\Delta G_{{37}}^{^\circ }$$ of the duplex formation with an error value of 10%. The high accuracy of predictive calculation for different types of natural complexes (DNA/RNA, DNA/RNA, and RNA/RNA) indicates the possibility of extending the considered approach to analogs and derivatives of nucleic acids, which gives a fundamental opportunity in the future to perform rational design of new types of NA-targeted sequence-specific compounds.
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Abdi SAH, Ali A, Sayed SF, Ahsan MJ, Tahir A, Ahmad W, Shukla S, Ali A. Morusflavone, a New Therapeutic Candidate for Prostate Cancer by CYP17A1 Inhibition: Exhibited by Molecular Docking and Dynamics Simulation. PLANTS 2021; 10:plants10091912. [PMID: 34579444 PMCID: PMC8468843 DOI: 10.3390/plants10091912] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/08/2021] [Accepted: 09/10/2021] [Indexed: 01/14/2023]
Abstract
Morusflavone, a flavonoid from Morus alba L., was evaluated for its interactive ability and stability with CYP17A1, in comparison with abiraterone, which is a Food and Drug Administration (FDA)-approved CYP17A1 inhibitor. CYP17A1 inhibition is an important therapeutic target for prostate cancer. The CHAMM36 force field was used to perform molecular dynamics (MD) simulations in this study. The results show that Morusflavone has significant interactive ability and stability for CYP17A1, in comparison with abiraterone. The final interaction energies for the Morusflavone–CYP17A1 and abiraterone–CYP17A1 complexes were −246.252 KJ/mol and −207.86 KJ/mol, respectively. Since there are only limited therapeutic agents available, such as abiraterone, galeterone, and seviteronel, which are being developed for prostate cancer, information on any potent natural anticancer compounds, such as vinca alkaloids, for prostate cancer treatment is limited. The results of this study show that CYP17A1 inhibition by Morusflavone could be an important therapeutic target for prostate cancer. Further preclinical and clinical evaluations of the lead compound Morusflavone are required to evaluate whether it can serve as a potential inhibitor of CYP17A1, which will be a new hope for prostate cancer treatment.
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Affiliation(s)
| | - Amena Ali
- Department of Pharmaceutical Chemistry, College of Pharmacy, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia;
| | - Shabihul Fatma Sayed
- Department of Nursing, University College Farasan Campus, Jazan University, Jazan 54943, Saudi Arabia;
| | - Mohamed Jawed Ahsan
- Department of Pharmaceutical Chemistry, Maharishi Arvind College of Pharmacy, Ambabari Circle, Jaipur 302 039, Rajasthan, India;
| | - Abu Tahir
- Department of Pharmacology, Raghukul College of Pharmacy, Bhopal 462 003, Madhya Pradesh, India;
| | - Wasim Ahmad
- Department of Pharmacy, Mohammed Al-Mana College for Medical Sciences, Dammam 34222, Saudi Arabia;
| | - Shatrunajay Shukla
- Indian Pharmacopoeia Commission, Ministry of Health & Family Welfare, Government of India, Ghaziabad 201002, Uttar Pradesh, India;
| | - Abuzer Ali
- Department of Pharmacognosy, College of Pharmacy, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
- Correspondence:
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Abdi SAH, Alzahrani A, Asad M, Alquraini A, Alghamdi AI, Sayed SF. Molecular docking and dynamics simulation to screen interactive potency and stability of fungicide tebuconazole with thyroid and sex hormone-binding globulin: Implications of endocrine and reproductive interruptions. J Appl Toxicol 2021; 41:1649-1659. [PMID: 33629778 DOI: 10.1002/jat.4153] [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] [Received: 12/28/2020] [Revised: 02/07/2021] [Accepted: 02/08/2021] [Indexed: 01/24/2023]
Abstract
Tebuconazole is a widely used fungicide in agriculture, and it may easily enter in the human food chain. In addition, tebuconzaol skin permeation coefficient (Log Kp) is -5.55 cm/s and it does not violate Lipinski's rule. It may mimic as a ligand for various endocrine and reproductive receptor leading to toxicological response or disease manifestation. We studied interactive potential of tebuconazole with thyroid and sex hormone-binding globulin. The main methods for this in silico analyses are molecular docking and molecular dynamic (MD) simulation. This paper explores how agriculture fungicide tebuconzaol exposure can be a risk for endocrine and reprotoxicity due to its stable interactive potency with thyroid and sex hormone-binding globulin (2CEO and 1D2S). Thyroid impairment is one of the most common endocrine issues in human health. In molecular docking analyses, tebuconazole exhibited binding potency of -6.28 kcal/mol with 2CEO compared to its native ligand thyroxin and inhibitor propylthiouracil which had the binding potency of -9.9 and -4.49 kcal/mol, respectively. The binding score of tebuconzaol with 1D2S was found to be -7.54 kcal/mol compared to native ligand dihydrotestosteron and inhibitor aminoglutethimide which exhibited the binding score of -6.84 and -11.41 kcal/mol, respectively. Therefore, each complex was subjected to MD simulation for comparative assessment of physical movement. The root mean square deviation (RMSD), root mean square fluctuation (RMSF), Radius of Gyration and hydrogen bonding exhibited that fluconazole had stable binding pattern with 2CEO and 1D2S which was almost similar to native ligand and its inhibitor. Study revealed that tebuconazole may lead to potent endocrine and reproductive disruptions.
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Affiliation(s)
| | | | - Mohammad Asad
- CEISAM, UMR CNRS 6230, Université de Nantes, BP 92208, 2, Rue de la Houssinière, 44322, Nantes Cedex 3, France
| | - Ali Alquraini
- Department of Pharmacy, Albaha University, Albaha, Kingdom of Saudi Arabia
| | | | - Shabihul Fatma Sayed
- Department of Nursing, University College Farasan Campus, Jazan University, Kingdom of Saudi Arabia
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Saini G, Dalal V, Gupta DN, Sharma N, Kumar P, Sharma AK. A molecular docking and dynamic approach to screen inhibitors against ZnuA1 of Candidatus Liberibacter asiaticus. MOLECULAR SIMULATION 2021. [DOI: 10.1080/08927022.2021.1888948] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Gunjan Saini
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Vikram Dalal
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Deena Nath Gupta
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Nidhi Sharma
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Pravindra Kumar
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Ashwani Kumar Sharma
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
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Raval B, Srivastav AK, Gupta SK, Kumar U, Mahapatra SK, Gajjar PN, Banerjee I. Synthesis of exfoliated multilayer graphene and its putative interactions with SARS-CoV-2 virus investigated through computational studies. J Biomol Struct Dyn 2020; 40:712-721. [PMID: 32914690 DOI: 10.1080/07391102.2020.1817788] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Our work investigates the interaction of synthesized graphene with the SARS-CoV-2 virus using molecular docking and molecular dynamics (MD) simulation method. The layer dependent inhibitory effect of graphene nanosheets on spike receptor-binding domain of 6LZG, complexed with host receptor i.e. angiotensin-converting enzyme 2 (ACE2) of SARS-CoV-2 was investigated through computational study. Graphene sample was synthesized using mechanical exfoliation with shear stress and its mechanism of inhibition towards the SARS-CoV-2 virus was explored by molecular docking and molecular dynamics (MD) simulation method. The thermodynamics study for the free binding energy of graphene towards the SARS-CoV-2 virus was analyzed. The binding energy of graphene towards the virus increased with an increasing number of layers. It shows the highest affinity of -17.5 Kcal/mol in molecular docking while ΔGbinding is in the order of -28.01 ± 0.04 5 Kcal/mol for the seven-layers structure. The increase in carbon layers is associated with an increasing number of edge sp3 -type carbon, providing greater curvature, further increase the surface reactivity responsible for high binding efficiency. The MD simulation data reveals the high inhibition efficiency of the synthesized graphene towards SARS-CoV-2 virus which would help to design future in-vitro studies. The graphene system could find potential applications in personal protective equipment and diagnostic kits.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Bhargav Raval
- School of Nano Sciences, Central University of Gujarat, Gandhinagar, India
| | | | - Sanjeev K Gupta
- Computational Materials and Nanoscience Group, Department of Physics, St. Xavier's College, Ahmedabad, India
| | - Umesh Kumar
- School of Nano Sciences, Central University of Gujarat, Gandhinagar, India
| | - S K Mahapatra
- Department of Physics, Central University of Punjab, Bathinda, India
| | - P N Gajjar
- Department of Physics, University School of Sciences, Gujarat University, Ahmedabad, India
| | - I Banerjee
- School of Nano Sciences, Central University of Gujarat, Gandhinagar, India
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Paul TJ, Vilseck JZ, Hayes RL, Brooks CL. Exploring pH Dependent Host/Guest Binding Affinities. J Phys Chem B 2020; 124:6520-6528. [PMID: 32628482 DOI: 10.1021/acs.jpcb.0c03671] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
When the electrostatic environment surrounding binding partners changes between unbound and bound states, the net uptake or release of a proton is possible by either binding partner. This process is pH-dependent in that the free energy required to uptake or release the proton varies with pH. This pH-dependence is typically not considered in conventional free energy methods where the use of fixed protonation states is the norm. In the present paper, we apply a simple two-step approach to calculate the pH-dependent binding free energy of a model cucubit[7]uril host/guest system. By use of λ-dynamics with an enhanced sampling protocol, adaptive landscape flattening, pKa shifts and reference binding free energies upon complexation were determined. This information enables the construction of pH-dependent binding profiles that accurately capture the pKa shifts and reproduce binding free energies at the different pH conditions that were observed experimentally. Our calculations illustrate a general framework for computing pH-dependent binding free energies but also point to some issues in modeling the molecular charge distributions within this series of molecules with CGenFF. However, by introducing some minor charge modifications to the CGenFF force field, we saw significant improvement in accuracy of the calculated pKa shifts.
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12
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Jamal S, Ahmed A, Moin ST. Evaluation of a sesquiterpene as possible drug lead against gelatinases via molecular dynamics simulations. J Biomol Struct Dyn 2020; 39:1645-1660. [PMID: 32174257 DOI: 10.1080/07391102.2020.1743363] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Malignant tumors can be targeted by accounting for their metastatic capabilities. Matrix metalloproteinases (MMPs) are the key players in tumor metastasis facilitating through their proteolytic activities of angiogenesis and extracellular matrix components (ECM) degradation. MMP-2 and MMP-9 being the members of a distinguished class of MMPs more commonly known as gelatinases are the prominent enzymes which are involved in different cancer progression stages. Targeting these isoforms specifically has always been a challenging task due to highly similar structural and functional features among the other members of MMPs with well preserve active sites containing catalytic zinc atom that was the only reason that none of the MMP inhibitor has been successfully marketed for the tumor pathology up till now. Therefore, non-competitive inhibitors with different structural attributed are needed to be evaluated at the molecular level for further experiments. The present study deals with the application of molecular dynamics simulation for the investigation of an alternative pathway for the inhibition of MMP-2 and MMP-9 by a sesquiterpene isolated from Polygonum barbatum which demonstrates the characteristics binding to the S1' subsite of the enzymes followed by in vitro gene expression studies. The simulation results provide information on the possible binding profile producing inhibitory effects imposed by the inhibitor to these enzymes by acquiring different structural and dynamical features. Moreover, thermodynamic quantities based on the computationally intensive thermodynamic integration approach were also obtained in terms of inhibitor binding affinity computed for the inhibitor against MMP-2 and MMP-9 that completely augmented the experimental gene expression study.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sehrish Jamal
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Ayaz Ahmed
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Syed Tarique Moin
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
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13
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Saini G, Dalal V, Savita BK, Sharma N, Kumar P, Sharma AK. Molecular docking and dynamic approach to virtual screen inhibitors against Esbp of Candidatus Liberibacter asiaticus. J Mol Graph Model 2019; 92:329-340. [PMID: 31446203 DOI: 10.1016/j.jmgm.2019.08.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 07/29/2019] [Accepted: 08/15/2019] [Indexed: 12/21/2022]
Abstract
Citrus greening (huanglongbing) is the most destructive disease of citrus worldwide caused by Candidatus Liberibacter asiaticus (CLA). Currently, no strategies have been developed to manage the Huanglongbing (HLB) disease and to stop the spreading of this disease to new citrus areas. Esbp is an extracellular solute-binding protein, involved in the uptake of iron in CLA. Thus, inhibiting this process may be a promising approach to design a drug against CLA. Thus, the present study focused on the identification of novel effective inhibitors which can inhibit the activity of CLas Esbp. A series of small molecules were screened against the CLas Esbp and the binding affinities were assessed using docking simulation studies. Top scored molecules were screened for different pharmacophore properties and Inhibitory Concentration 50 (IC50) values. Density functional theory was employed to check the chemical properties of the molecules. Further, Molecular Dynamics simulation analysis like RMSD, RMSF, Rg, SASA and MMPBSA results reveal that the identified molecules (ZINC03143779, ZINC05491830, ZINC19210425, ZINC08750867, and ZINC14671545) exhibit a good binding affinity for CLas Esbp and results in the formation of stable CLas Esbp-inhibitor(s) complex. The present study reported that these compounds appeared to be the suitable novel inhibitor of CLas Esbp and pave the way to further development of antimicrobial agents against CLA.
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Affiliation(s)
- Gunjan Saini
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247 667, India
| | - Vikram Dalal
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247 667, India
| | - Brajesh Kumar Savita
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247 667, India
| | - Nidhi Sharma
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247 667, India
| | - Pravindra Kumar
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247 667, India
| | - Ashwani Kumar Sharma
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247 667, India.
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14
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Garton M, Corbi-Verge C, Hu Y, Nim S, Tarasova N, Sherborne B, Kim PM. Rapid and accurate structure-based therapeutic peptide design using GPU accelerated thermodynamic integration. Proteins 2019; 87:236-244. [PMID: 30520126 DOI: 10.1002/prot.25644] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 10/30/2018] [Accepted: 11/29/2018] [Indexed: 11/07/2022]
Abstract
Peptide-based therapeutics are an alternative to small molecule drugs as they offer superior specificity, lower toxicity, and easy synthesis. Here we present an approach that leverages the dramatic performance increase afforded by the recent arrival of GPU accelerated thermodynamic integration (TI). GPU TI facilitates very fast, highly accurate binding affinity optimization of peptides against therapeutic targets. We benchmarked TI predictions using published peptide binding optimization studies. Prediction of mutations involving charged side-chains was found to be less accurate than for non-charged, and use of a more complex 3-step TI protocol was found to boost accuracy in these cases. Using the 3-step protocol for non-charged side-chains either had no effect or was detrimental. We use the benchmarked pipeline to optimize a peptide binding to our recently discovered cancer target: EME1. TI calculations predict beneficial mutations using both canonical and non-canonical amino acids. We validate these predictions using fluorescence polarization and confirm that binding affinity is increased. We further demonstrate that this increase translates to a significant reduction in pancreatic cancer cell viability.
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Affiliation(s)
- Michael Garton
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
| | - Carles Corbi-Verge
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
| | - Yuan Hu
- Merck & Co., Inc., Kenilworth, New Jersey.,Alkermes Inc., Waltham, Massachusetts
| | - Satra Nim
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
| | - Nadya Tarasova
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, Maryland
| | | | - Philip M Kim
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada.,Department of Computer Science, University of Toronto, Toronto, Canada
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15
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Pandit S, Dalal V, Mishra G. Identification of novel phosphatidic acid binding domain on sphingosine kinase 1 of Arabidopsis thaliana. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 128:178-184. [PMID: 29783183 DOI: 10.1016/j.plaphy.2018.04.039] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 04/25/2018] [Accepted: 04/27/2018] [Indexed: 06/08/2023]
Abstract
Phosphatidic acid (PA) is an important lipid signaling molecule which interacts with Arabidopsis thaliana Sphingosine kinase1 (AtSPHK1) during several abiotic stresses particularly drought stress as a result of Abscisic acid (ABA) signaling in guard cells. PA molecules respond by generating lipid signal and/or by binding and translocating target proteins to membrane. However, site of interaction and role of PA binding to AtSPHK1 is not clear yet. Owing to the importance of AtSPHK1 during stress signaling it is imperative to decipher the site of PA interaction with AtSPHK1. To identify the PA binding region of AtSPHK1, various deletion fragments from N-terminal and C-terminal region were prepared. Results from protein lipid overlay assay using various truncated proteins of AtSPHK1 suggested the involvement of N-terminal region, between 110 and 205 amino acids, in binding with PA. In-silico analyses performed to build homologous structure of AtSPHK1 revealed that PA docking occurs in the hydrophobic cavity of DAG-Kinase domain. Deletion of amino acids 182VSGDGI187 perturbed PA-AtSPHK1 binding, indicating an essential role of these six amino acids in PA-AtSPHK1 binding.
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Affiliation(s)
- Shatakshi Pandit
- - Department of Botany, University of Delhi, Delhi 110007, India
| | - Vikram Dalal
- - Department of Biotechnology, Indian Institute of Technology, Roorkee, Uttarakhand 247667, India
| | - Girish Mishra
- - Department of Botany, University of Delhi, Delhi 110007, India.
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16
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Mermelstein DJ, Lin C, Nelson G, Kretsch R, McCammon JA, Walker RC. Fast and flexible gpu accelerated binding free energy calculations within the amber molecular dynamics package. J Comput Chem 2018. [PMID: 29532496 DOI: 10.1002/jcc.25187] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Alchemical free energy (AFE) calculations based on molecular dynamics (MD) simulations are key tools in both improving our understanding of a wide variety of biological processes and accelerating the design and optimization of therapeutics for numerous diseases. Computing power and theory have, however, long been insufficient to enable AFE calculations to be routinely applied in early stage drug discovery. One of the major difficulties in performing AFE calculations is the length of time required for calculations to converge to an ensemble average. CPU implementations of MD-based free energy algorithms can effectively only reach tens of nanoseconds per day for systems on the order of 50,000 atoms, even running on massively parallel supercomputers. Therefore, converged free energy calculations on large numbers of potential lead compounds are often untenable, preventing researchers from gaining crucial insight into molecular recognition, potential druggability and other crucial areas of interest. Graphics Processing Units (GPUs) can help address this. We present here a seamless GPU implementation, within the PMEMD module of the AMBER molecular dynamics package, of thermodynamic integration (TI) capable of reaching speeds of >140 ns/day for a 44,907-atom system, with accuracy equivalent to the existing CPU implementation in AMBER. The implementation described here is currently part of the AMBER 18 beta code and will be an integral part of the upcoming version 18 release of AMBER. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Daniel J Mermelstein
- Department of Chemistry & Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California, 92093
| | - Charles Lin
- Department of Chemistry & Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California, 92093.,GlaxoSmithKline PLC, 1250 S. Collegeville Rd, Collegeville, Pennsylvania, 19426
| | - Gard Nelson
- NantBioscience, Inc., 9920 Jefferson Boulevard, Culver City, California, 90232
| | - Rachael Kretsch
- Department of Chemistry & Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California, 92093.,Harvey Mudd College, 301 Platt Blvd, Claremont, California, 91711
| | - J Andrew McCammon
- Department of Chemistry & Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California, 92093
| | - Ross C Walker
- Department of Chemistry & Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California, 92093.,GlaxoSmithKline PLC, 1250 S. Collegeville Rd, Collegeville, Pennsylvania, 19426
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17
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Singh N, Dalal V, Kumar P. Structure based mimicking of Phthalic acid esters (PAEs) and inhibition of hACMSD, an important enzyme of the tryptophan kynurenine metabolism pathway. Int J Biol Macromol 2018; 108:214-224. [DOI: 10.1016/j.ijbiomac.2017.12.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 12/01/2017] [Accepted: 12/03/2017] [Indexed: 10/18/2022]
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18
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A computational approach for designing D-proteins with non-canonical amino acid optimised binding affinity. PLoS One 2017; 12:e0187524. [PMID: 29108013 PMCID: PMC5673230 DOI: 10.1371/journal.pone.0187524] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Accepted: 10/21/2017] [Indexed: 01/08/2023] Open
Abstract
Redesigning protein surface topology to improve target binding holds great promise in the search for highly selective therapeutics. While significant binding improvements can be achieved using natural amino acids, the introduction of non-canonical residues vastly increases sequence space and thus the chance to significantly out-compete native partners. The potency of protein inhibitors can be further enhanced by synthesising mirror image, D-amino versions. This renders them non-immunogenic and makes them highly resistant to proteolytic degradation. Current experimental design methods often preclude the use of D-amino acids and non-canonical amino acids for a variety of reasons. To address this, we build an in silico pipeline for D-protein designs featuring non-canonical amino acids. For a test scaffold we use an existing D-protein inhibitor of VEGF: D-RFX001. We benchmark the approach by recapitulating previous experimental optimisation with canonical amino acids. Subsequent incorporation of non-canonical amino acids allows designs that are predicted to improve binding affinity by up to -7.18 kcal/mol.
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19
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Williams-Noonan BJ, Yuriev E, Chalmers DK. Free Energy Methods in Drug Design: Prospects of “Alchemical Perturbation” in Medicinal Chemistry. J Med Chem 2017; 61:638-649. [DOI: 10.1021/acs.jmedchem.7b00681] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Billy J. Williams-Noonan
- Medicinal Chemistry, Monash
Institute of Pharmaceutical Sciences, Monash University, 381 Royal
Parade, Parkville, Victoria 3052, Australia
| | - Elizabeth Yuriev
- Medicinal Chemistry, Monash
Institute of Pharmaceutical Sciences, Monash University, 381 Royal
Parade, Parkville, Victoria 3052, Australia
| | - David K. Chalmers
- Medicinal Chemistry, Monash
Institute of Pharmaceutical Sciences, Monash University, 381 Royal
Parade, Parkville, Victoria 3052, Australia
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20
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Thirumal Kumar D, Lavanya P, George Priya Doss C, Tayubi IA, Naveen Kumar DR, Francis Yesurajan I, Siva R, Balaji V. A Molecular Docking and Dynamics Approach to Screen Potent Inhibitors Against Fosfomycin Resistant Enzyme in Clinical Klebsiella pneumoniae. J Cell Biochem 2017; 118:4088-4094. [PMID: 28409871 DOI: 10.1002/jcb.26064] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 04/13/2017] [Indexed: 01/13/2023]
Abstract
Klebsiella pneumoniae, BA6753 was cultured from a patient in the Clinical Microbiology Laboratory of Christian Medical College. K. pneumoniae, BA6753 has a multidrug resistance plasmid encoding novel FosA variant-7, fosfomycin resistance enzyme. Minimal side effects and a wide range of bactericidal activity of fosfomycin have resulted in its expanded clinical use that prompts the rise of fosfomycin-resistant strains. At present, there are no effective inhibitors available to conflict the FosA-medicated fosfomycin resistance. To develop effective FosA inhibitors, it is crucial to understand the structural and dynamic properties of resistance enzymes. Hence, the present study focuses on the identification of potent inhibitors that can effectively bind to the fosfomycin resistance enzyme, thus predispose the target to inactivate by the second antibiotic. Initially, a series of active compounds were screened against the resistant enzyme, and the binding affinities were confirmed using docking simulation analysis. For efficient activity, the binding affinity of the resistance enzyme ought to be high with the inhibitor than the fosfomycin drug. Consequently, the enzyme-ligand complex which showed higher binding affinity than the fosfomycin was employed for subsequent analysis. The stability of the top scoring enzyme-ligand complex was further validated using molecular dynamics simulation studies. On the whole, we presume that the compound 19583672 demonstrates a higher binding affinity for the resistance enzyme comparing to other compounds and fosfomycin. We believe that further enhancement of the lead compound can serve as a potential inhibitor against resistance enzyme in drug discovery process. J. Cell. Biochem. 118: 4088-4094, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- D Thirumal Kumar
- School of Biosciences and Technology, VIT University, Vellore, 632014, India
| | - P Lavanya
- Department of Clinical Microbiology, Christian Medical College, Vellore, 632004, India
| | - C George Priya Doss
- School of Biosciences and Technology, VIT University, Vellore, 632014, India
| | - Iftikhar Aslam Tayubi
- Faculty of Computing and Information Technology, King Abdulaziz University, Rabigh, 21911, Saudi Arabia
| | - D R Naveen Kumar
- Department of Clinical Microbiology, Christian Medical College, Vellore, 632004, India
| | - I Francis Yesurajan
- Department of Clinical Microbiology, Christian Medical College, Vellore, 632004, India
| | - R Siva
- School of Biosciences and Technology, VIT University, Vellore, 632014, India
| | - V Balaji
- Department of Clinical Microbiology, Christian Medical College, Vellore, 632004, India
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21
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Hsu CJ, Hsu WC, Lee DJ, Liu AL, Chang CM, Shih HJ, Huang WH, Lee-Chen GJ, Hsieh-Li HM, Lee GC, Sun YC. Investigation of the bindings of a class of inhibitors with GSK3β kinase using thermodynamic integration MD simulation and kinase assay. Chem Biol Drug Des 2017; 90:272-281. [PMID: 28127860 DOI: 10.1111/cbdd.12946] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Revised: 12/09/2016] [Accepted: 01/05/2017] [Indexed: 01/08/2023]
Abstract
GSK3β kinase is a noteworthy target for discovery of the drugs that will be used to treat several diseases. In the effort to identify a new inhibitor lead compound, we utilized thermodynamic integration (TI)-molecular dynamics (MD) simulation and kinase assay to investigate the bindings between GSK3β kinase and five compounds that were analogous to a known inhibitor with an available crystal structure. TI-MD simulations of the first two compounds (analogs 1 and 2) were used for calibration. The computed binding affinities of analogs 1 and 2 agreed well with the experimental results. The rest three compounds (analogs 3-5) were newly obtained from a database search, and their affinity data were newly measured in our labs. TI-MD simulations predicted the binding modes and the computed ΔΔG values have a reasonably good correlation with the experimental affinity data. These newly identified inhibitors appear to be new leads according to our survey of GSK3β inhibitors listed in recent review articles. The predicted binding modes of these compounds should aid in designing new derivatives of these compounds in the future.
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Affiliation(s)
- Chia-Jen Hsu
- Department of Chemistry, National Taiwan Normal University, Taipei, Taiwan
| | - Wen-Chi Hsu
- Department of Chemistry, National Taiwan Normal University, Taipei, Taiwan
| | - Der-Jay Lee
- Department of Chemistry, National Taiwan Normal University, Taipei, Taiwan
| | - An-Lun Liu
- Department of Chemistry, National Taiwan Normal University, Taipei, Taiwan
| | - Chia-Ming Chang
- Department of Chemistry, National Taiwan Normal University, Taipei, Taiwan
| | - Huei-Jhen Shih
- Department of Chemistry, National Taiwan Normal University, Taipei, Taiwan
| | - Wun-Han Huang
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Guey-Jen Lee-Chen
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Hsiu Mei Hsieh-Li
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Guan-Chiun Lee
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Ying-Chieh Sun
- Department of Chemistry, National Taiwan Normal University, Taipei, Taiwan
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22
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Alchemical determination of drug-receptor binding free energy: Where we stand and where we could move to. J Mol Graph Model 2017; 71:233-241. [DOI: 10.1016/j.jmgm.2016.11.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 11/24/2016] [Accepted: 11/29/2016] [Indexed: 01/05/2023]
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23
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Lavanya P, Ramaiah S, Anbarasu A. A Molecular Docking and Dynamics Study to Screen Potent Anti-Staphylococcal Compounds Against Ceftaroline Resistant MRSA. J Cell Biochem 2016; 117:542-8. [PMID: 26252252 DOI: 10.1002/jcb.25307] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 07/28/2015] [Indexed: 01/16/2023]
Abstract
World Health Organization reports that methicillin-resistant Staphylococcus aureus (MRSA) is the origin of higher proportion of hospital acquired infections. In order to combat the effect of MRSA infection, an ideal drug should stimulate the allosteric exposure of active site, prompting penicillin binding proteins (PBP2a) to bind with that particular compound. Ceftaroline shows high binding affinity towards PBP2a and also confers resistance against degrading enzymes. Recently, two amino acid alterations in the allosteric site of PBP2a, asparagine (N) to lysine (K) at position 146 and glutamic acid (E) to lysine at position 150 are reported to confer resistance against ceftaroline resulting in the rise of ceftaroline-resistant MRSA strains. The present study focuses on the identification of potential ligands that can effectively bind with allosteric site of PBP2a, that leads to the access of active site and entry of a β-lactam antibiotic for effective inhibition. The results obtained from our study will be useful for designing effective compounds with potential therapeutic effects against ceftaroline resistant MRSA strains.
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Affiliation(s)
- P Lavanya
- Medical & Biological Computing Laboratory, School of Biosciences and Technology, VIT University, Vellore, 632014, Tamil Nadu, India
| | - Sudha Ramaiah
- Medical & Biological Computing Laboratory, School of Biosciences and Technology, VIT University, Vellore, 632014, Tamil Nadu, India
| | - Anand Anbarasu
- Medical & Biological Computing Laboratory, School of Biosciences and Technology, VIT University, Vellore, 632014, Tamil Nadu, India
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24
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Lavanya P, Ramaiah S, Anbarasu A. Ethyl 4-(4-methylphenyl)-4-pentenoate from Vetiveria zizanioides Inhibits Dengue NS2B-NS3 Protease and Prevents Viral Assembly: A Computational Molecular Dynamics and Docking Study. Cell Biochem Biophys 2016; 74:337-51. [PMID: 27324039 DOI: 10.1007/s12013-016-0741-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 06/09/2016] [Indexed: 12/16/2022]
Abstract
Around 50 % of the world's population is at the risk of dengue, a viral infection. Presently, there are not many drugs and prophylactic measures available to control dengue viral infection, and hence, there is an urgent need to develop effective antidengue compound from natural sources. In the current study, we explored the antiviral properties of the medicinal plant Vetiveria zizanioides against dengue virus. Initially, the antiviral properties of active compounds were examined using docking analysis along with reference ligand. The enzyme-ligand complex which showed higher binding affinity than the reference ligand was employed for subsequent analysis. The stability of the top scoring enzyme-ligand complex was further validated using molecular simulation studies. On the whole, the study reveals that the compound Ethyl 4-(4-methylphenyl)-4-pentenoate has an effective antiviral property, which can serve as a potential lead molecule in drug discovery process.
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Affiliation(s)
- P Lavanya
- Medical & Biological Computing Laboratory, School of Biosciences and Technology, VIT University, Vellore, 632014, Tamil Nadu, India
| | - Sudha Ramaiah
- Medical & Biological Computing Laboratory, School of Biosciences and Technology, VIT University, Vellore, 632014, Tamil Nadu, India
| | - Anand Anbarasu
- Medical & Biological Computing Laboratory, School of Biosciences and Technology, VIT University, Vellore, 632014, Tamil Nadu, India.
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25
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Arfeen M, Patel R, Khan T, Bharatam PV. Molecular dynamics simulation studies of GSK-3β ATP competitive inhibitors: understanding the factors contributing to selectivity. J Biomol Struct Dyn 2015. [PMID: 26209183 DOI: 10.1080/07391102.2015.1063457] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Glycogen synthase kinase-3 is a constitutively acting, multifunctional serine threonine kinase, the role of which has been implicated in several physiological pathways and has emerged as a promising target for the treatment of type-II diabetes and Alzheimer's disease. In order to provide a detailed understanding of the origin of selectivity determinants of ATP competitive inhibitors, molecular dynamics simulations in combination with MM-PBSA binding energy calculations were performed using crystal structures of GSK-3β and CDK-2 in complex with 12 ATP competitive inhibitors. Analysis of energy contributions indicate that electrostatic interaction energy dictates the selectivity of ATP competitive inhibitors against CDK-2. Key interactions as well as residues that potentially make a major contribution to the binding free energy were identified at the ATP binding site. This analysis stresses the need for the inhibitors to interact with Lys85, Thr138, and Arg141 in the binding site of GSK-3β to show selectivity. The residue-wise energy decomposition analysis further suggested the additional role of Gln185 in determining the selectivity of maleimides. The results obtained in this study can be utilized to design new selective GSK-3 ATP competitive inhibitors.
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Affiliation(s)
- Minhajul Arfeen
- a Department of Medicinal Chemistry , National Institute of Pharmaceutical Education and Research , Sector-67, S.A.S. Nagar, Punjab 160062 , India
| | - Rahul Patel
- a Department of Medicinal Chemistry , National Institute of Pharmaceutical Education and Research , Sector-67, S.A.S. Nagar, Punjab 160062 , India
| | - Tosif Khan
- a Department of Medicinal Chemistry , National Institute of Pharmaceutical Education and Research , Sector-67, S.A.S. Nagar, Punjab 160062 , India
| | - Prasad V Bharatam
- a Department of Medicinal Chemistry , National Institute of Pharmaceutical Education and Research , Sector-67, S.A.S. Nagar, Punjab 160062 , India
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26
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Sun YC, Hsu WC, Hsu CJ, Chang CM, Cheng KH. Investigation of differences in the binding affinities of two analogous ligands for untagged and tagged p38 kinase using thermodynamic integration MD simulation. J Mol Model 2015; 21:283. [PMID: 26450350 DOI: 10.1007/s00894-015-2825-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 09/22/2015] [Indexed: 11/26/2022]
Abstract
Thermodynamic integration (TI) molecular dynamics (MD) simulations for the binding of a pair of a reference ("ref") ligand and an analogous ("analog") ligand to either tagged (with six extra residues at the N-terminus) or untagged p38 kinase proteins were carried out in order to probe how the binding affinity is influenced by the presence or absence of the peptide tag in p38 kinase. This possible effect of protein length on the binding affinity of a ligand-which is seldom addressed in the literature-is important because, even when two labs claim to have performed experiments with the same protein, they may actually have studied variants of the same protein with different lengths because they applied different protein expression conditions/procedures. Thus, if we wanted to compare ligand binding affinities measured in the two labs, it would be necessary to account for any variation in ligand binding affinity with protein length. The pair of ligand-p38 kinase complexes examined in this work (pdb codes: 3d7z and 3lhj, respectively) were ideal for investigating this effect. The experimentally determined binding energy for the ref ligand with the untagged p38 kinase was -10.9 kcal mol(-1), while that for the analog ligand with the tagged p38 kinase was -11.9 kcal mol(-1). The present TI-MD simulation of the mutation of the ref ligand into the analog ligand while the ligand is bound to the untagged p38 kinase predicted that the binding affinity of the analog ligand is 2.0 kcal mol(-1) greater than that of the ref ligand. A similar simulation also indicated that the same was true for ligand binding to the tagged protein, but in this case the binding affinity for the analog ligand is 2.5 kcal mol(-1) larger than that for the ref ligand. These results therefore suggest that the presence of the peptide tag on p38 kinase increased the difference in the binding energies of the ligands by a small amount of 0.5 kcal mol(-1). This result supports the assumption that the presence of a peptide tag has only a minor effect on ΔG values. The error bars in the computed ΔG values were then estimated via confidence interval analysis and a time autocorrelation function for the quantity dV/dλ. The estimated correlation time was ~0.5 ps and the error bar in the ΔG values estimated using nanosecond-scale simulations was ±0.3 kcal mol(-1) at a confidence level of 95%. These predicted results can be verified in future experiments and should prove useful in subsequent similar studies. Graphical Abstract Thermodynamic cycles for binding of two analogous ligands with untagged and tagged p38 kinases and associated Gibbs free energy.
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Affiliation(s)
- Ying-Chieh Sun
- Department of Chemistry, National Taiwan Normal University, 88, TingChow Road Section 4, Taipei, 116, Taiwan, Republic of China.
| | - Wen-Chi Hsu
- Department of Chemistry, National Taiwan Normal University, 88, TingChow Road Section 4, Taipei, 116, Taiwan, Republic of China
| | - Chia-Jen Hsu
- Department of Chemistry, National Taiwan Normal University, 88, TingChow Road Section 4, Taipei, 116, Taiwan, Republic of China
| | - Chia-Ming Chang
- Department of Chemistry, National Taiwan Normal University, 88, TingChow Road Section 4, Taipei, 116, Taiwan, Republic of China
| | - Kai-Hsiang Cheng
- Department of Chemistry, National Taiwan Normal University, 88, TingChow Road Section 4, Taipei, 116, Taiwan, Republic of China
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27
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Zhan M, Guo M, Jiang Y, Wang X. Characterization of the Interaction between Gallic Acid and Lysozyme by Molecular Dynamics Simulation and Optical Spectroscopy. Int J Mol Sci 2015; 16:14786-807. [PMID: 26140374 PMCID: PMC4519872 DOI: 10.3390/ijms160714786] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Revised: 06/08/2015] [Accepted: 06/17/2015] [Indexed: 01/29/2023] Open
Abstract
The binding interaction between gallic acid (GA) and lysozyme (LYS) was investigated and compared by molecular dynamics (MD) simulation and spectral techniques. The results from spectroscopy indicate that GA binds to LYS to generate a static complex. The binding constants and thermodynamic parameters were calculated. MD simulation revealed that the main driving forces for GA binding to LYS are hydrogen bonding and hydrophobic interactions. The root-mean-square deviation verified that GA and LYS bind to form a stable complex, while the root-mean-square fluctuation results showed that the stability of the GA-LYS complex at 298 K was higher than that at 310 K. The calculated free binding energies from the molecular mechanics/Poisson-Boltzmann surface area method showed that van der Waals forces and electrostatic interactions are the predominant intermolecular forces. The MD simulation was consistent with the spectral experiments. This study provides a reference for future study of the pharmacological mechanism of GA.
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Affiliation(s)
- Minzhong Zhan
- School of Science, Zhejiang Agricultural & Forestry University, Lin'an 311300, China.
| | - Ming Guo
- School of Science, Zhejiang Agricultural & Forestry University, Lin'an 311300, China.
| | - Yanke Jiang
- Research Center of Medical Chemistry & Chemical Biology, Chongqing Technology and Business University, Chongqing 400067, China.
| | - Xiaomeng Wang
- School of Science, Zhejiang Agricultural & Forestry University, Lin'an 311300, China.
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