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Chakraborty A, Ghosh R, Barik S, Mohapatra SS, Biswas A, Chowdhuri S. Deciphering inhibitory activity of marine algae Ecklonia cava phlorotannins against SARS CoV-2 main protease: A coupled in-silico docking and molecular dynamics simulation study. Gene 2024; 926:148620. [PMID: 38821329 DOI: 10.1016/j.gene.2024.148620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/21/2024] [Accepted: 05/28/2024] [Indexed: 06/02/2024]
Abstract
The onset of COVID-19 due to the SARS CoV-2 virus has spurred an urgent need for potent therapeutics and vaccines to combat this global pandemic. The main protease (Mpro) of the virus, crucial in its replication, has become a focal point in developing anti-COVID-19 drugs. The cysteine protease Mpro in SARS CoV-2 bears a significant resemblance to the same protease found in SARS CoV-1. Previous research highlighted phlorotannins derived from Ecklonia cava, an edible marine algae, as inhibitors of SARS CoV-1 Mpro activity. However, it remains unclear whether these marine-derived phlorotannins also exert a similar inhibitory effect on SARS CoV-2 Mpro. To unravel this, our study utilized diverse in-silico methodologies. We explored the pharmacological potential of various phlorotannins (phloroglucinol, triphloretol-A, eckol, 2-phloroeckol, 7-phloroeckol, fucodiphloroethol G, dieckol, and phlorofucofuroeckol-A) and assessed their binding efficacies alongside established Mpro inhibitors (N3 and lopinavir) through molecular docking studies. Among these compounds, five phlorotannins (eckol, 2-phloroeckol, 7-phloroeckol, dieckol, and phlorofucofuroeckol-A) exhibited potent binding affinities comparable to or surpassing N3 and lopinavir, interacting especially with the catalytic residues His41 and Cys145 of Mpro. Moreover, molecular dynamics simulations revealed that these five Mpro-phlorotannin complexes displayed enhanced stability and maintained comparable or slightly reduced compactness. They exhibited reduced conformational changes and increased expansion relative to the Mpro-N3 and/or Mpro-lopinavir complex. Our MM-GBSA analysis further supported these findings. Overall, our investigation highlights the potential of these five phlorotannins in inhibiting the proteolytic function of SARS CoV-2 Mpro, offering promise for anti-COVID-19 drug development.
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Affiliation(s)
- Ayon Chakraborty
- University Institute of Biotechnology, University Centre for Research & Development, Chandigarh University, Mohali, India
| | - Rajesh Ghosh
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | - Subhashree Barik
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | | | - Ashis Biswas
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India.
| | - Snehasis Chowdhuri
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India.
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2
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Chakraborty A, Ghosh R, Soumya Mohapatra S, Barik S, Biswas A, Chowdhuri S. Repurposing of antimycobacterium drugs for COVID-19 treatment by targeting SARS CoV-2 main protease: An in-silico perspective. Gene 2024; 922:148553. [PMID: 38734190 DOI: 10.1016/j.gene.2024.148553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 04/27/2024] [Accepted: 05/08/2024] [Indexed: 05/13/2024]
Abstract
The global mortality rate has been significantly impacted by the COVID-19 pandemic, caused by the SARS CoV-2 virus. Although the pursuit for a potent antiviral is still in progress, experimental therapies based on repurposing of existing drugs is being attempted. One important therapeutic target for COVID-19 is the main protease (Mpro) that cleaves the viral polyprotein in its replication process. Recently minocycline, an antimycobacterium drug, has been successfully implemented for the treatment of COVID-19 patients. But it's mode of action is still far from clear. Furthermore, it remains unresolved whether alternative antimycobacterium drugs can effectively regulate SARS CoV-2 by inhibiting the enzymatic activity of Mpro. To comprehend these facets, eight well-established antimycobacterium drugs were put through molecular docking experiments. Four of the antimycobacterium drugs (minocycline, rifampicin, clofazimine and ofloxacin) were selected by comparing their binding affinities towards Mpro. All of the four drugs interacted with both the catalytic residues of Mpro (His41 and Cys145). Additionally, molecular dynamics experiments demonstrated that the Mpro-minocyline complex has enhanced stability, experiences reduced conformational fluctuations and greater compactness than other three Mpro-antimycobacterium and Mpro-N3/lopinavir complexes. This research furnishes evidences for implementation of minocycline against SARS CoV-2. In addition, our findings also indicate other three antimycobacterium/antituberculosis drugs (rifampicin, clofazimine and ofloxacin) could potentially be evaluated for COVID-19 therapy.
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Affiliation(s)
- Ayon Chakraborty
- University Institute of Biotechnology, University Centre for Research & Development, Chandigarh University, Mohali, India
| | - Rajesh Ghosh
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | | | - Subhashree Barik
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | - Ashis Biswas
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India.
| | - Snehasis Chowdhuri
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India.
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3
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Nayana P, Gollapalli P, Manjunatha H. Investigating the structural basis of piperine targeting AKT1 against prostate cancer through in vitro and molecular dynamics simulations. J Biomol Struct Dyn 2024:1-15. [PMID: 38529821 DOI: 10.1080/07391102.2024.2331096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 03/11/2024] [Indexed: 03/27/2024]
Abstract
AkT1, significantly impacts many tumours cell functions, like transcription, apoptosis, glucose metabolism, cell proliferation, and cell migration. For tumours to develop and spread, aberrant activation of AKT1 is essential. Therefore, a major focus of molecularly targeted PCa treatment is AKT1. The present study investigates the effect of piperine compared to SDF using in-vitro studies, viz colony formation assay, comet assay and AKT1 gene expression studies using human PCa cell line PC3. A cluster of approximately at least 50 cells constitutes a colony. The clonogenic assay showed that the number and size of colonies significantly decreased when treated with compounds (SDF and piperine) in comparison to the untreated cells which effectively proliferated to form more colonies. Piperine treatment showed significant inhibition of colony formation than SDF. Effective genotoxicity was observed in piperine-treated PC3 cells with an increased Tail length of 120 µm and it was moderately observed in SDF with a Tail length of 30 µm treated on PC3 cells. The control group did not show any considerable genotoxicity with a Tail length of 6 µm. Our data, both in vitro and in silico, suggested that piperine would be a good starting point for developing novel drugs for the treatment of PCa. The downstream functions of Akt1 may be inhibited by these effects, which could impede the proliferation of PCa cells. High stability of the piperine-AKT1 complex was found by the MD simulation. Higher hydrophilic residues like Lys268 and Ser205 at the active pocket may be the cause of the binding stability. Overall, the observed results confirmed the anti-PCa effect of piperine by causing effective DNA damage and proved to be genotoxic in nature against the human PCa. These effects may impede the downstream activities of Akt1 and result in PCa cell growth regression.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Prakash Nayana
- Department of PG Studies and Research in Biotechnology, Kuvempu University, Shivamogga, Karnataka, India
| | - Pavan Gollapalli
- Center for Bioinformatics and Biostatistics, Nitte (Deemed to be University), Mangalore, Karnataka, India
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4
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Rahimi M, Taghdir M, Abasi Joozdani F. Dynamozones are the most obvious sign of the evolution of conformational dynamics in HIV-1 protease. Sci Rep 2023; 13:14179. [PMID: 37648682 PMCID: PMC10469195 DOI: 10.1038/s41598-023-40818-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 08/17/2023] [Indexed: 09/01/2023] Open
Abstract
Proteins are not static but are flexible molecules that can adopt many different conformations. The HIV-1 protease is an important target for the development of therapies to treat AIDS, due to its critical role in the viral life cycle. We investigated several dynamics studies on the HIV-1 protease families to illustrate the significance of examining the dynamic behaviors and molecular motions for an entire understanding of their dynamics-structure-function relationships. Using computer simulations and principal component analysis approaches, the dynamics data obtained revealed that: (i) The flap regions are the most obvious sign of the evolution of conformational dynamics in HIV-1 protease; (ii) There are dynamic structural regions in some proteins that contribute to the biological function and allostery of proteins via appropriate flexibility. These regions are a clear sign of the evolution of conformational dynamics of proteins, which we call dynamozones. The flap regions are one of the most important dynamozones members that are critical for HIV-1 protease function. Due to the existence of other members of dynamozones in different proteins, we propose to consider dynamozones as a footprint of the evolution of the conformational dynamics of proteins.
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Affiliation(s)
- Mohammad Rahimi
- Department of Biophysics, Faculty of Biological Science, Tarbiat Modares University, Tehran, 14115_111, Iran
| | - Majid Taghdir
- Department of Biophysics, Faculty of Biological Science, Tarbiat Modares University, Tehran, 14115_111, Iran.
| | - Farzane Abasi Joozdani
- Department of Biophysics, Faculty of Biological Science, Tarbiat Modares University, Tehran, 14115_111, Iran
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5
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Yang F, Wang Y, Yan D, Liu Z, Wei B, Chen J, He W. Binding Mechanism of Inhibitors to Heat Shock Protein 90 Investigated by Multiple Independent Molecular Dynamics Simulations and Prediction of Binding Free Energy. Molecules 2023; 28:4792. [PMID: 37375347 DOI: 10.3390/molecules28124792] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/09/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
The heat shock protein (HSP90) has been an import target of drug design in the treatment of human disease. An exploration of the conformational changes in HSP90 can provide useful information for the development of efficient inhibitors targeting HSP90. In this work, multiple independent all-atom molecular dynamics (AAMD) simulations followed by calculations of the molecular mechanics generalized Born surface area (MM-GBSA) were performed to explore the binding mechanism of three inhibitors (W8Y, W8V, and W8S) to HSP90. The dynamics analyses verified that the presence of inhibitors impacts the structural flexibility, correlated movements, and dynamics behavior of HSP90. The results of the MM-GBSA calculations suggest that the selection of GB models and empirical parameters has important influences on the predicted results and verify that van der Waals interactions are the main forces that determine inhibitor-HSP90 binding. The contributions of separate residues to the inhibitor-HSP90 binding process indicate that hydrogen-bonding interactions (HBIs) and hydrophobic interactions play important roles in HSP90-inhibitor identifications. Moreover, residues L34, N37, D40, A41, D79, I82, G83, M84, F124, and T171 are recognized as hot spots of inhibitor-HSP90 binding and provide significant target sites of for the design of drugs related to HSP90. This study aims to contribute to the development of efficient inhibitors that target HSP90 by providing an energy-based and theoretical foundation.
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Affiliation(s)
- Fen Yang
- School of Information Science and Electrical Engineering, Shandong Jiaotong University, Jinan 250357, China
| | - Yiwen Wang
- School of Information Science and Electrical Engineering, Shandong Jiaotong University, Jinan 250357, China
- School of Aeronautics, Shandong Jiaotong University, Jinan 250357, China
| | - Dongliang Yan
- School of Information Science and Electrical Engineering, Shandong Jiaotong University, Jinan 250357, China
- School of Science, Shandong Jiaotong University, Jinan 250357, China
| | - Zhongtao Liu
- School of Information Science and Electrical Engineering, Shandong Jiaotong University, Jinan 250357, China
| | - Benzheng Wei
- Center for Medical Artificial Intelligence, Shandong University of Traditional Chinese Medicine, Qingdao 266112, China
| | - Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan 250357, China
| | - Weikai He
- School of Aeronautics, Shandong Jiaotong University, Jinan 250357, China
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6
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Wang L, Wang Y, Yu Y, Liu D, Zhao J, Zhang L. Deciphering Selectivity Mechanism of BRD9 and TAF1(2) toward Inhibitors Based on Multiple Short Molecular Dynamics Simulations and MM-GBSA Calculations. Molecules 2023; 28:molecules28062583. [PMID: 36985555 PMCID: PMC10052767 DOI: 10.3390/molecules28062583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/06/2023] [Accepted: 03/09/2023] [Indexed: 03/14/2023] Open
Abstract
BRD9 and TAF1(2) have been regarded as significant targets of drug design for clinically treating acute myeloid leukemia, malignancies, and inflammatory diseases. In this study, multiple short molecular dynamics simulations combined with the molecular mechanics generalized Born surface area method were employed to investigate the binding selectivity of three ligands, 67B, 67C, and 69G, to BRD9/TAF1(2) with IC50 values of 230/59 nM, 1400/46 nM, and 160/410 nM, respectively. The computed binding free energies from the MM-GBSA method displayed good correlations with that provided by the experimental data. The results indicate that the enthalpic contributions played a critical factor in the selectivity recognition of inhibitors toward BRD9 and TAF1(2), indicating that 67B and 67C could more favorably bind to TAF1(2) than BRD9, while 69G had better selectivity toward BRD9 over TAF1(2). In addition, the residue-based free energy decomposition approach was adopted to calculate the inhibitor–residue interaction spectrum, and the results determined the gatekeeper (Y106 in BRD9 and Y1589 in TAF1(2)) and lipophilic shelf (G43, F44, and F45 in BRD9 and W1526, P1527, and F1528 in TAF1(2)), which could be identified as hotspots for designing efficient selective inhibitors toward BRD9 and TAF1(2). This work is also expected to provide significant theoretical guidance and insightful molecular mechanisms for the rational designs of efficient selective inhibitors targeting BRD9 and TAF1(2).
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Yu YX, Wang W, Sun HB, Zhang LL, Wang LF, Yin YY. Decoding drug resistant mechanism of V32I, I50V and I84V mutations of HIV-1 protease on amprenavir binding by using molecular dynamics simulations and MM-GBSA calculations. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2022; 33:805-831. [PMID: 36322686 DOI: 10.1080/1062936x.2022.2140708] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Mutations V32I, I50V and I84V in the HIV-1 protease (PR) induce drug resistance towards drug amprenavir (APV). Multiple short molecular dynamics (MSMD) simulations and molecular mechanics generalized Born surface area (MM-GBSA) method were utilized to investigate drug-resistant mechanism of V32I, I50V and I84V towards APV. Dynamic information arising from MSMD simulations suggest that V32I, I50V and I84V highly affect structural flexibility, motion modes and conformational behaviours of two flaps in the PR. Binding free energies calculated by MM-GBSA method suggest that the decrease in binding enthalpy and the increase in binding entropy induced by mutations V32I, I50V and I84V are responsible for drug resistance of the mutated PRs on APV. The energetic contributions of separate residues on binding of APV to the PR show that V32I, I50V and I84V highly disturb the interactions of two flaps with APV and mostly drive the decrease in binding ability of APV to the PR. Thus, the conformational changes of two flaps in the PR caused by V32I, I50V and I84V play key roles in drug resistance of three mutated PR towards APV. This study can provide useful dynamics information for the design of potent inhibitors relieving drug resistance.
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Affiliation(s)
- Y X Yu
- School of Science, Shandong Jiaotong University, Jinan, China
| | - W Wang
- School of Science, Shandong Jiaotong University, Jinan, China
| | - H B Sun
- School of Science, Shandong Jiaotong University, Jinan, China
| | - L L Zhang
- School of Science, Shandong Jiaotong University, Jinan, China
| | - L F Wang
- School of Science, Shandong Jiaotong University, Jinan, China
| | - Y Y Yin
- School of Science, Shandong Jiaotong University, Jinan, China
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8
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Ghosh R, Chakraborty A, Biswas A, Chowdhuri S. Computer aided identification of potential SARS CoV-2 main protease inhibitors from diterpenoids and biflavonoids of Torreya nucifera leaves. J Biomol Struct Dyn 2022; 40:2647-2662. [PMID: 33140695 PMCID: PMC7663460 DOI: 10.1080/07391102.2020.1841680] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 10/19/2020] [Indexed: 12/23/2022]
Abstract
SARS CoV-2 is the causative agent of the pandemic disease COVID-19. There is an urgent need for effective drugs or vaccines which can effectively combat this outbreak. The main protease (Mpro), a key component for the SARS CoV-2 replication, is considered to be one of the important drug targets for developing anti-COVID-19 drugs. This SARS CoV-2 Mpro/cysteine protease has high sequence similarity with the same protease from SARS CoV-1. Previously, it has been shown experimentally that eight diterpenoids and four biflavonoids derived from the leaf of Torreya nucifera show inhibitory effect on the cleavage/catalytic activity of the SARS CoV-1 Mpro. But whether these phytochemicals exhibit any inhibitory effect on SARS CoV-2 Mpro is unclear. To understand this fact, here, we have adopted various in-silico approaches. Diterpenoids and biflavonoids those qualified pharmacological test (hinokiol, amentoflavone, bilobetin and ginkgetin) and two well-known Mpro inhibitors (N3 and lopinavir) were subjected for molecular docking studies. Only three biflavonoids (amentoflavone, bilobetin and ginkgetin) were selected by comparing their binding affinities with N3 and lopinavir. They interacted with two most important catalytic residues of Mpro (His41 and Cys145). Molecular dynamics studies further revealed that these three Mpro-biflavonoid complexes are highly stable and share a similar degree of compactness. Besides, these complexes experience less conformational fluctuations and more expansion than Mpro-N3 and/or Mpro-lopinavir complex. MM-GBSA and H-bond analysis further corroborated these findings. Altogether, our study suggested that these three biflavonoids could possibly inhibit the proteolytic/catalytic activity of SARS CoV-2 Mpro and might be useful for COVID-19 treatment.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rajesh Ghosh
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | - Ayon Chakraborty
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | - Ashis Biswas
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | - Snehasis Chowdhuri
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
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Rizzuti B. Molecular simulations of proteins: From simplified physical interactions to complex biological phenomena. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140757. [PMID: 35051666 DOI: 10.1016/j.bbapap.2022.140757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 01/08/2022] [Accepted: 01/10/2022] [Indexed: 12/22/2022]
Abstract
Molecular dynamics simulation is the most popular computational technique for investigating the structural and dynamical behaviour of proteins, in search of the molecular basis of their function. Far from being a completely settled field of research, simulations are still evolving to best capture the essential features of the atomic interactions that govern a protein's inner motions. Modern force fields are becoming increasingly accurate in providing a physical description adequate to this purpose, and allow us to model complex biological systems under fairly realistic conditions. Furthermore, the use of accelerated sampling techniques is improving our access to the observation of progressively larger molecular structures, longer time scales, and more hidden functional events. In this review, the basic principles of molecular dynamics simulations and a number of key applications in the area of protein science are summarized, and some of the most important results are discussed. Examples include the study of the structure, dynamics and binding properties of 'difficult' targets, such as intrinsically disordered proteins and membrane receptors, and the investigation of challenging phenomena like hydration-driven processes and protein aggregation. The findings described provide an overall picture of the current state of this research field, and indicate new perspectives on the road ahead to the upcoming future of molecular simulations.
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Affiliation(s)
- Bruno Rizzuti
- CNR-NANOTEC, SS Rende (CS), Department of Physics, University of Calabria, 87036 Rende, Italy; Institute for Biocomputation and Physics of Complex Systems (BIFI), Joint Unit GBsC-CSIC-BIFI, University of Zaragoza, 50018 Zaragoza, Spain.
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10
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Ghosh R, Chakraborty A, Biswas A, Chowdhuri S. Identification of alkaloids from Justicia adhatoda as potent SARS CoV-2 main protease inhibitors: An in silico perspective. J Mol Struct 2021; 1229:129489. [PMID: 33100380 PMCID: PMC7571971 DOI: 10.1016/j.molstruc.2020.129489] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/17/2020] [Accepted: 10/18/2020] [Indexed: 01/08/2023]
Abstract
The COVID-19 pandemic, caused by SARS CoV-2, is responsible for millions of death worldwide. No approved/proper therapeutics is currently available which can effectively combat this outbreak. Several attempts have been undertaken in the search of effective drugs to control the spread of SARS CoV-2 infection. The main protease (Mpro), key component for the cleavage of the viral polyprotein, is considered to be one of the important drug targets for treating COVID-19. Various phytochemicals, including polyphenols and alkaloids, have been proposed as potent inhibitors of Mpro. The alkaloids from leaf extracts of Justicia adhatoda have also been reported to possess anti-viral activity. But whether these alkaloids exhibit any inhibitory effect on SARS CoV-2 Mpro is far from clear. To explore this in detail, we have adopted computational approaches. Justicia adhatoda alkaloids possessing proper drug-likeness properties and two anti-HIV drugs (lopinavir and darunavir; having binding affinity -7.3 to -7.4 kcal/mol) were docked against SARS CoV-2 Mpro to study their binding properties. Only one alkaloid (anisotine) had interaction with both the catalytic residues (His41 and Cys145) of Mpro and exhibited good binding affinity (-7.9 kcal/mol). Molecular dynamic simulations (100 ns) revealed that Mpro-anisotine complex is more stable, conformationally less fluctuated; slightly less compact and marginally expanded than Mpro-darunavir/lopinavir complex. Even the number of intermolecular H-bonds and MM-GBSA analysis suggested that anisotine is a more potent Mpro inhibitor than the two previously recommended antiviral drugs (lopinavir and darunavir) and may evolve as a promising anti-COVID-19 drug if proven in animal experiments and on patients.
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Affiliation(s)
- Rajesh Ghosh
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | - Ayon Chakraborty
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | - Ashis Biswas
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | - Snehasis Chowdhuri
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
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11
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Ghosh R, Chakraborty A, Biswas A, Chowdhuri S. Depicting the inhibitory potential of polyphenols from Isatis indigotica root against the main protease of SARS CoV-2 using computational approaches. J Biomol Struct Dyn 2020; 40:4110-4121. [PMID: 33292085 PMCID: PMC7738210 DOI: 10.1080/07391102.2020.1858164] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The pandemic disease COVID-19, caused by SARS CoV-2, has created a global crisis. Presently, researchers across the globe are in a quest to identify/develop drugs or vaccines by targeting different non-structural proteins (Nsps) of SARS CoV-2. One such important drug target is Nsp5/main protease (Mpro) which plays a critical role in the viral replication. This cysteine protease/Mpro of SARS CoV-2 has high sequence similarity with the same protease from SARS CoV-1. Previously, it has been shown experimentally that eight polyphenols derived from the root of Isatis indigotica show inhibitory effect on the cleavage/catalytic activity of the SARS CoV-1 Mpro. But whether these polyphenols exhibit any inhibitory effect on SARS CoV-2 Mpro is unclear. To explore this possibility, here, we have adopted various computational approaches. Polyphenols that qualified the pharmacological parameters (indigo, sinigrin, hesperetin and daidzein) and two well-known Mpro inhibitors (N3 and lopinavir) were subjected to molecular docking studies. Two of them (sinigrin and hesperetin) were selected by comparing their binding affinities with N3 and lopinavir. Sinigrin and hesperetin interacted with the two most important catalytic residues of Mpro (His41 and Cys145). Molecular dynamics studies further revealed that these two Mpro-polyphenol complexes are more stable and experience less conformational fluctuations than Mpro-N3/lopinavir complex. The Mpro-hesperetin complex was more compact and less expanded than Mpro-sinigrin complex. These findings were additionally validated by MM-GBSA analysis. As a whole, our study revealed that these two polyphenols may be potent SARS CoV-2 Mpro inhibitors and may possibly be considered for COVID-19 treatment.
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Affiliation(s)
- Rajesh Ghosh
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | - Ayon Chakraborty
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | - Ashis Biswas
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | - Snehasis Chowdhuri
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
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12
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Ghosh R, Chakraborty A, Biswas A, Chowdhuri S. Identification of polyphenols from Broussonetia papyrifera as SARS CoV-2 main protease inhibitors using in silico docking and molecular dynamics simulation approaches. J Biomol Struct Dyn 2020; 39:6747-6760. [PMID: 32762411 PMCID: PMC7484588 DOI: 10.1080/07391102.2020.1802347] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The current COVID-19 pandemic is caused by SARS CoV-2. To date, ∼463,000 people died
worldwide due to this disease. Several attempts have been taken in search of effective
drugs to control the spread of SARS CoV-2 infection. The main protease (Mpro) from SARS
CoV-2 plays a vital role in viral replication and thus serves as an important drug target.
This Mpro shares a high degree of sequence similarity (>96%) with the same protease
from SARS CoV-1 and MERS. It was already reported that Broussonetia
papyrifera polyphenols efficiently inhibit the catalytic activity of SARS CoV-1
and MERS Mpro. But whether these polyphenols exhibit any inhibitory effect on SARS CoV-2
Mpro is far from clear. To understand this fact, here we have adopted computational
approaches. Polyphenols having proper drug-likeness properties and two repurposed drugs
(lopinavir and darunavir; having binding affinity −7.3 to −7.4 kcal/mol) were docked
against SARS CoV-2 Mpro to study their binding properties. Only six polyphenols
(broussochalcone A, papyriflavonol A, 3'-(3-methylbut-2-enyl)-3',4',7-trihydroxyflavane,
broussoflavan A, kazinol F and kazinol J) had interaction with both the
catalytic residues (His41 and Cys145) of Mpro and exhibited good binding affinity (−7.6 to
−8.2 kcal/mol). Molecular dynamic simulations (100 ns) revealed that all Mpro-polyphenol
complexes are more stable, conformationally less fluctuated; slightly less compact and
marginally expanded than Mpro-darunavir/lopinavir complex. Even the number of
intermolecular H-bond and MM-GBSA analysis suggested that these six polyphenols are more
potent Mpro inhibitors than the two repurposed drugs (lopinavir and darunavir) and may
serve as promising anti-COVID-19 drugs. Communicated by Ramaswamy H. Sarma
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Affiliation(s)
- Rajesh Ghosh
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | - Ayon Chakraborty
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | - Ashis Biswas
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | - Snehasis Chowdhuri
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
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13
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Sk MF, Jonniya NA, Kar P. Exploring the energetic basis of binding of currently used drugs against HIV-1 subtype CRF01_AE protease via molecular dynamics simulations. J Biomol Struct Dyn 2020; 39:5892-5909. [DOI: 10.1080/07391102.2020.1794965] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Md Fulbabu Sk
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Nisha Amarnath Jonniya
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Parimal Kar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
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14
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Ghosh R, Chakraborty A, Biswas A, Chowdhuri S. Evaluation of green tea polyphenols as novel corona virus (SARS CoV-2) main protease (Mpro) inhibitors - an in silico docking and molecular dynamics simulation study. J Biomol Struct Dyn 2020; 39:4362-4374. [PMID: 32568613 PMCID: PMC7332865 DOI: 10.1080/07391102.2020.1779818] [Citation(s) in RCA: 143] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Coronavirus disease 2019 (COVID-19) is a viral respiratory disease which caused global health emergency and announced as pandemic disease by World Health Organization. Lack of specific drug molecules or treatment strategy against this disease makes it more devastating. Thus, there is an urgent need of effective drug molecules to fight against COVID-19. The main protease (Mpro) of SARS CoV-2, a key component of this viral replication, is considered as a prime target for anti-COVID-19 drug development. In order to find potent Mpro inhibitors, we have selected eight polyphenols from green tea, as these are already known to exert antiviral activity against many RNA viruses. We have elucidated the binding affinities and binding modes between these polyphenols including a well-known Mpro inhibitor N3 (having binding affinity -7.0 kcal/mol) and Mpro using molecular docking studies. All eight polyphenols exhibit good binding affinity toward Mpro (-7.1 to -9.0 kcal/mol). However, only three polyphenols (epigallocatechin gallate, epicatechingallate and gallocatechin-3-gallate) interact strongly with one or both catalytic residues (His41 and Cys145) of Mpro. Molecular dynamics simulations (100 ns) on these three Mpro-polyphenol systems further reveal that these complexes are highly stable, experience less conformational fluctuations and share similar degree of compactness. Estimation of total number of intermolecular H-bond and MM-GBSA analysis affirm the stability of these three Mpro-polyphenol complexes. Pharmacokinetic analysis additionally suggested that these polyphenols possess favorable drug-likeness characteristics. Altogether, our study shows that these three polyphenols can be used as potential inhibitors against SARS CoV-2 Mpro and are promising drug candidates for COVID-19 treatment.
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Affiliation(s)
- Rajesh Ghosh
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | - Ayon Chakraborty
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | - Ashis Biswas
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | - Snehasis Chowdhuri
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
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15
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Mechanism of inhibition of drug-resistant HIV-1 protease clinical isolates by TMC310911: A molecular dynamics study. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.126893] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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16
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Yan F, Liu X, Zhang S, Zhang Q, Chen J. Understanding conformational diversity of heat shock protein 90 (HSP90) and binding features of inhibitors to HSP90 via molecular dynamics simulations. Chem Biol Drug Des 2019; 95:87-103. [PMID: 31560152 DOI: 10.1111/cbdd.13623] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 08/06/2019] [Accepted: 08/26/2019] [Indexed: 12/23/2022]
Abstract
Heat shock protein 90 (HSP90) is a promising target for treatment of cancer, and inhibitor bindings can generate efficient suppression on tumor in multiple ways. In this work, 140-ns molecular dynamics simulations were performed on six systems. Principal component analysis was subsequently carried out to explore the conformational diversity of HSP90. The results suggest that inhibitor bindings induce large conformational changes of HSP90, which tends to enlarge the volume of the binding pocket to facilitate the entrance of inhibitors. Hierarchical clustering analyses, the calculation of the energy contribution of each atom, and the analyses of hydrogen-bonding interactions were performed. The results indicate that 20 residues in group A of the hierarchical tree are responsible for major contributions, and van der Waals interactions as well as hydrogen-bonding interactions between important residues in HSP90 and key regions of inhibitors are the main force for promoting inhibitor bindings. We expect that this work can provide useful theoretical information for development of efficient inhibitors targeting HSP90.
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Affiliation(s)
- Fangfang Yan
- School of Physics and Electronics, Shandong Normal University, Jinan, China
| | - Xinguo Liu
- School of Physics and Electronics, Shandong Normal University, Jinan, China
| | - Shaolong Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan, China
| | - Qinggang Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan, China
| | - Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan, China
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17
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Insights into the binding mechanisms of inhibitors of MDM2 based on molecular dynamics simulations and binding free energy calculations. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2019.05.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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18
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Structural studies of antiviral inhibitor with HIV-1 protease bearing drug resistant substitutions of V32I, I47V and V82I. Biochem Biophys Res Commun 2019; 514:974-978. [PMID: 31092330 DOI: 10.1016/j.bbrc.2019.05.064] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 05/07/2019] [Indexed: 12/23/2022]
Abstract
HIV-1 protease inhibitors are effective in HIV/AIDS therapy, although drug resistance is a severe problem. This study examines the effects of four investigational inhibitors against HIV-1 protease with drug resistant mutations of V32I, I47V and V82I (PRTri) that model the inhibitor-binding site of HIV-2 protease. These inhibitors contain diverse chemical modifications on the darunavir scaffold and form new interactions with wild type protease, however, the measured inhibition constants for PRTri mutant range from 17 to 40 nM or significantly worse than picomolar values reported for wild type enzyme. The X-ray crystal structure of PRTri mutant in complex with inhibitor 1 at 1.5 Å resolution shows minor changes in interactions with inhibitor compared with the corresponding wild type PR complex. Instead, the basic amine at P2 of inhibitor together with mutation V82I induces two alternate conformations for the side chain of Arg8 with new interactions with inhibitor and Leu10. Hence, inhibition is influenced by small coordinated changes in hydrophobic interactions.
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19
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Molecular alteration in drug susceptibility against subtype B and C-SA HIV-1 proteases: MD study. Struct Chem 2019. [DOI: 10.1007/s11224-019-01305-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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20
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C.S. V, Tamizhselvi R, Munusami P. Exploring the drug resistance mechanism of active site, non-active site mutations and their cooperative effects in CRF01_AE HIV-1 protease: molecular dynamics simulations and free energy calculations. J Biomol Struct Dyn 2019; 37:2608-2626. [DOI: 10.1080/07391102.2018.1492459] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Vasavi C.S.
- School of Biosciences and Technology, VIT University, Vellore, India
| | | | - Punnagai Munusami
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, India
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21
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Yan F, Liu X, Zhang S, Su J, Zhang Q, Chen J. Effect of double mutations T790M/L858R on conformation and drug-resistant mechanism of epidermal growth factor receptor explored by molecular dynamics simulations. RSC Adv 2018; 8:39797-39810. [PMID: 35558225 PMCID: PMC9091310 DOI: 10.1039/c8ra06844e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 11/18/2018] [Indexed: 12/28/2022] Open
Abstract
Epidermal growth factor receptor (EGFR) is one of the most promising targets for the treatment of cancers. Double mutations T790M/L858R lead to different degrees of drug resistance toward inhibitors. In this study, molecular dynamics (MD) simulations followed by principal component analysis are performed to study the conformational changes of EGFR induced by T790M/L858R. The results suggest that T790M/L858R cause obvious disturbance of the structural stability of EGFR. Molecular mechanics-Poisson Boltzmann surface area (MM-PBSA) and residue-based free energy decomposition methods are integrated to explore the drug-resistant mechanism of T790M/L858R toward inhibitors. The results show that the decrease in van der Waals interactions of inhibitors with the mutated EFGR relative to the wild-type (WT) one is the main force inducing drug resistance of T790M/L858R toward inhibitors TAK-285, while drug resistance toward W2P and HKI-272 is dominated by the decrease in van der Waals interactions and the increase in polar interactions. We expect that the information obtained from this study can aid rational design of effective drugs to relieve drug resistance of EGFR induced by T790M/L858R.
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Affiliation(s)
- Fangfang Yan
- School of Physics and Electronics, Shandong Normal University Jinan 250358 China
| | - Xinguo Liu
- School of Physics and Electronics, Shandong Normal University Jinan 250358 China
| | - Shaolong Zhang
- School of Physics and Electronics, Shandong Normal University Jinan 250358 China
| | - Jing Su
- School of Physics and Electronics, Shandong Normal University Jinan 250358 China
| | - Qinggang Zhang
- School of Physics and Electronics, Shandong Normal University Jinan 250358 China
| | - Jianzhong Chen
- School of Science, Shandong Jiaotong University Jinan 250357 China
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22
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Maphumulo SI, Halder AK, Govender T, Maseko S, Maguire GEM, Honarparvar B, Kruger HG. Exploring the flap dynamics of the South African HIV subtype C protease in presence of FDA-approved inhibitors: MD study. Chem Biol Drug Des 2018; 92:1899-1913. [PMID: 30003668 DOI: 10.1111/cbdd.13364] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 07/09/2018] [Indexed: 01/01/2023]
Abstract
HIV-1 protease (HIV PR) is considered as one of the most attractive targets for the treatment of HIV and the impact of flap dynamics of HIV PR on the binding affinities of protease inhibitors (PIs) is a crucial ongoing research field. Recently, our research group evaluated the binding affinities of different FDA approved PIs against the South African HIV-1 subtype C (C-SA) protease (PR). The CSA-HIV PR displayed weaker binding affinity for most of the clinical PIs compared to HIV-1 B subtype for West and Central Europe, the Americas. In the current work, the flap dynamics of four different systems of HIV-1 C-SA PR complexed to FDA approved second generation PIs and its impact on binding was explored over the molecular dynamic trajectories. It was observed that the interactions of the selected drugs with the binding site residues of the protease may not be the major contributor for affinity towards PIs. Various post-MD analyses were performed, also entropic contributions, solvation free energies and hydrophobic core formation interactions were studied to assess how the flap dynamics of C-SA PR which is affected by such factors. From these contributions, large van der Waals interactions and low solvation free energies were found to be major factors for the higher activity of ATV against C-SA HIV PR. Furthermore, a comparatively stable hydrophobic core may be responsible for higher stability of the PR flaps of the ATV complex. The outcome of this study provides significant guidance to how the flap dynamics of C-SA PR is affected by various factors as a result of the binding affinity of various protease inhibitors. It will also assist with the design of potent inhibitors against C-SA HIV PR that apart from binding in the active site of PR can interacts with the flaps to prevent opening of the flaps resulting in inactivation of the protease.
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Affiliation(s)
- Siyabonga I Maphumulo
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Amit K Halder
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Thavendran Govender
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Sibusiso Maseko
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Glenn E M Maguire
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.,School of Chemistry and Physics, University of KwaZulu-Natal, Durban, South Africa
| | - Bahareh Honarparvar
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Hendrik G Kruger
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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23
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Yan F, Liu X, Zhang S, Su J, Zhang Q, Chen J. Molecular Dynamics Exploration of Selectivity of Dual Inhibitors 5M7, 65X, and 65Z toward Fatty Acid Binding Proteins 4 and 5. Int J Mol Sci 2018; 19:ijms19092496. [PMID: 30142969 PMCID: PMC6164837 DOI: 10.3390/ijms19092496] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 08/14/2018] [Accepted: 08/18/2018] [Indexed: 12/11/2022] Open
Abstract
Designing highly selective inhibitors of fatty acid binding proteins 4 and 5 (FABP4 and FABP5) is of importance for treatment of some diseases related with inflammation, metabolism, and tumor growth. In this study, molecular dynamics (MD) simulations combined with molecular mechanics generalized Born surface area (MM-GBSA) method were performed to probe binding selectivity of three inhibitors (5M7, 65X, and 65Z) to FABP4/FABP5 with Ki values of 0.022/0.50 μM, 0.011/0.086 μM, and 0.016/0.12 μM, respectively. The results not only suggest that all inhibitors associate more tightly with FABP4 than FABP5, but also prove that the main forces driving the selective bindings of inhibitors to FABP4 and FABP5 stem from the difference in the van der Waals interactions and polar interactions of inhibitors with two proteins. Meanwhile, a residue-based free energy decomposition method was applied to reveal molecular basis that inhibitors selectively interact with individual residues of two different proteins. The calculated results show that the binding difference of inhibitors to the residues (Phe16, Phe19), (Ala33, Gly36), (Phe57, Leu60), (Ala75, Ala78), (Arg126, Arg129), and (Tyr128, Tyr131) in (FABP4, FABP5) drive the selectivity of inhibitors toward FABP4 and FABP5. This study will provide great help for further design of effective drugs to protect against a series of metabolic diseases, arteriosclerosis, and inflammation.
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Affiliation(s)
- Fangfang Yan
- School of Physics and Electronics, Shandong Normal University, Jinan 250358, China.
| | - Xinguo Liu
- School of Physics and Electronics, Shandong Normal University, Jinan 250358, China.
| | - Shaolong Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan 250358, China.
| | - Jing Su
- School of Physics and Electronics, Shandong Normal University, Jinan 250358, China.
| | - Qinggang Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan 250358, China.
| | - Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan 250357, China.
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24
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Gao Y, Zhu T, Chen J. Exploring drug-resistant mechanisms of I84V mutation in HIV-1 protease toward different inhibitors by thermodynamics integration and solvated interaction energy method. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.06.040] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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25
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Chen J, Wang J, Zhu W. Zinc ion-induced conformational changes in new Delphi metallo-β-lactamase 1 probed by molecular dynamics simulations and umbrella sampling. Phys Chem Chem Phys 2018; 19:3067-3075. [PMID: 28079218 DOI: 10.1039/c6cp08105c] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The hydrolysis of a β-lactam core ring caused by new Delphi metallo-β-lactamase 1 (NDM-1) with the help of two zinc cofactors induces significant resistance toward β-lactam antibiotics. Molecular dynamics (MD) simulations and the umbrella sampling method are integrated to study the conformational change mechanism of NDM-1 mediated by zinc ion binding. The statistical analyses of interaction contacts of the antibiotic ampicillin (AMP) with residues based on MD trajectories suggest that two Zn ions are essential for maintaining the binding of AMP with NDM-1. Umbrella sampling simulations further reveal that double-Zn coordination exerts strong restriction on the motions of loop L10 relative to loops L3 and L4. Principal component (PC) analysis also demonstrates that zinc ion binding totally inhibits the motion extent of NDM-1 and changes internal motion modes in NDM-1. We expect that the current study can provide significant dynamical information involving conformational changes of NDM-1 for the development of efficient inhibitors to decrease drug resistance of NDM-1 toward antibiotics.
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Affiliation(s)
- Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan, 250014, China.
| | - Jinan Wang
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China.
| | - Weiliang Zhu
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China.
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26
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Wang C, Greene D, Xiao L, Qi R, Luo R. Recent Developments and Applications of the MMPBSA Method. Front Mol Biosci 2018; 4:87. [PMID: 29367919 PMCID: PMC5768160 DOI: 10.3389/fmolb.2017.00087] [Citation(s) in RCA: 316] [Impact Index Per Article: 52.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 11/30/2017] [Indexed: 12/23/2022] Open
Abstract
The Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) approach has been widely applied as an efficient and reliable free energy simulation method to model molecular recognition, such as for protein-ligand binding interactions. In this review, we focus on recent developments and applications of the MMPBSA method. The methodology review covers solvation terms, the entropy term, extensions to membrane proteins and high-speed screening, and new automation toolkits. Recent applications in various important biomedical and chemical fields are also reviewed. We conclude with a few future directions aimed at making MMPBSA a more robust and efficient method.
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Affiliation(s)
- Changhao Wang
- Chemical and Materials Physics Graduate Program, University of California, Irvine, Irvine, CA, United States
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
- Department of Physics and Astronomy, University of California, Irvine, Irvine, CA, United States
| | - D'Artagnan Greene
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Li Xiao
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, United States
| | - Ruxi Qi
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Ray Luo
- Chemical and Materials Physics Graduate Program, University of California, Irvine, Irvine, CA, United States
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, United States
- Department of Chemical Engineering and Materials Science, University of California, Irvine, Irvine, CA, United States
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27
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Chen J, Wang J, Lai F, Wang W, Pang L, Zhu W. Dynamics revelation of conformational changes and binding modes of heat shock protein 90 induced by inhibitor associations. RSC Adv 2018; 8:25456-25467. [PMID: 35539786 PMCID: PMC9082529 DOI: 10.1039/c8ra05042b] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 07/10/2018] [Indexed: 11/21/2022] Open
Abstract
Heat shock protein 90 (Hsp90) has been an attractive target of potential drug design for antitumor treatment. The current work integrates molecular dynamics (MD) simulations, calculations of binding free energy, and principal component (PC) analysis with scanning of inhibitor–residue interaction to probe the binding modes of inhibitors YK9, YKJ and YKI to Hsp90 and identify the hot spot of the inhibitor–Hsp90 binding. The results suggest that the introductions of two groups G1 and G2 into YKJ and YKI strengthen the binding ability of YKJ and YKI to Hsp90 compared to YK9. PC analysis based MD trajectories prove that inhibitor bindings exert significant effects on the conformational changes, internal dynamics and motion modes of Hsp90, especially for the helix α2 and the loops L1 and L2. The calculations of residue-based free energy decomposition and scanning of the inhibitor–Hsp90 interaction suggest that six residues L107, G108, F138, Y139, W162 and F170 construct the common hot spot of the inhibitor–residue interactions. Moreover the substitutions of the groups G1 and G2 in YKJ and YKI lead to two additional hydrogen bonding interactions and multiple hydrophobic interactions for bindings of YKJ and YKI to Hsp90. This work is also expected to contribute theoretical hints for the design of potent inhibitors toward Hsp90. Heat shock protein 90 (Hsp90) has been an attractive target of potential drug design for antitumor treatment.![]()
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Affiliation(s)
- Jianzhong Chen
- School of Science
- Shandong Jiaotong University
- Jinan
- China
- Drug Discovery and Design Center
| | - Jinan Wang
- Drug Discovery and Design Center
- CAS Key Laboratory of Receptor Research
- Shanghai Institute of Materia Medica
- Chinese Academy of Sciences
- Shanghai
| | - Fengbo Lai
- School of Science
- Shandong Jiaotong University
- Jinan
- China
| | - Wei Wang
- School of Science
- Shandong Jiaotong University
- Jinan
- China
| | - Laixue Pang
- School of Science
- Shandong Jiaotong University
- Jinan
- China
| | - Weiliang Zhu
- Drug Discovery and Design Center
- CAS Key Laboratory of Receptor Research
- Shanghai Institute of Materia Medica
- Chinese Academy of Sciences
- Shanghai
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28
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Huang X, Xu P, Cao Y, Liu L, Song G, Xu L. Exploring the binding mechanisms of PDE5 with chromeno[2,3-c]pyrrol-9(2H)-one by theoretical approaches. RSC Adv 2018; 8:30481-30490. [PMID: 35546827 PMCID: PMC9085377 DOI: 10.1039/c8ra06405a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 08/17/2018] [Indexed: 01/10/2023] Open
Abstract
Cyclic nucleotide phosphodiesterase type 5 (PDE5), exclusively specific for the cyclic guanosine monophosphate (cGMP), is an important drug target for the treatment of erectile dysfunction and pulmonary arterial hypertension (PAH). Although many PDE5 inhibitors have been approved, such as sildenafil, vardenafil, tadalafil and so on, extensive studies have reported some side effects, such as vision disturbance and hearing loss as a result of the amino acid sequence and the secondary structural similarity of other PDEs to the catalytic domain of PDE5. In this study, multiple docking strategies, molecular dynamics (MD) simulations, free energy calculations and decomposition were employed to explore the structural determinants of PDE5 with a series of chromeno[2,3-c]pyrrol-9(2H)-one derivatives. First, reliable docking results were obtained using quantum mechanics/molecular mechanics (QM/MM) docking. Then, MD simulations and MM/GBSA free energy calculations were used to explore the dynamic binding process and characterize the binding modes of the inhibitors with different activities. The predicted binding free energies are in good agreement with the experimental data, and the MM/GBSA free energy decomposition analysis sheds light on the importance of hydrogen bonds with Gln817, π–π stacks against Phe820 and hydrophobic residues for the PDE5 binding of the studied inhibitors. The structural and energetic insights obtained here are useful for understanding the molecular mechanism of ligand binding and designing novel potent and selective PDE5 inhibitors with new scaffolds. Cyclic nucleotide phosphodiesterase type 5 (PDE5) is exclusively specific for the cyclic guanosine monophosphate (cGMP), and PDE5 is an important drug target for the treatment of erectile dysfunction and pulmonary arterial hypertension (PAH).![]()
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Affiliation(s)
- Xianfeng Huang
- School of Pharmaceutical Engineering and Life Sciences
- Changzhou University
- Changzhou
- PR China
| | - Peng Xu
- Department of Orthopedics
- Second Military Medical University Affiliated Changzheng Hospital
- Shanghai
- China
| | - Yijing Cao
- School of Pharmaceutical Engineering and Life Sciences
- Changzhou University
- Changzhou
- PR China
| | - Li Liu
- School of Pharmaceutical Engineering and Life Sciences
- Changzhou University
- Changzhou
- PR China
| | - Guoqiang Song
- School of Pharmaceutical Engineering and Life Sciences
- Changzhou University
- Changzhou
- PR China
| | - Lei Xu
- Institute of Bioinformatics and Medical Engineering
- School of Electrical and Information Engineering
- Jiangsu University of Technology
- Changzhou 213001
- China
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29
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Su J, Liu X, Zhang S, Yan F, Zhang Q, Chen J. A theoretical insight into selectivity of inhibitors toward two domains of bromodomain-containing protein 4 using molecular dynamics simulations. Chem Biol Drug Des 2017; 91:828-840. [DOI: 10.1111/cbdd.13148] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Revised: 10/22/2017] [Accepted: 11/01/2017] [Indexed: 12/16/2022]
Affiliation(s)
- Jing Su
- School of Physics and Electronics; Shandong Normal University; Jinan China
| | - Xinguo Liu
- School of Physics and Electronics; Shandong Normal University; Jinan China
| | - Shaolong Zhang
- School of Physics and Electronics; Shandong Normal University; Jinan China
| | - Fangfang Yan
- School of Physics and Electronics; Shandong Normal University; Jinan China
| | - Qinggang Zhang
- School of Physics and Electronics; Shandong Normal University; Jinan China
| | - Jianzhong Chen
- School of Science; Shandong Jiaotong University; Jinan China
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30
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Appadurai R, Senapati S. How Mutations Can Resist Drug Binding yet Keep HIV-1 Protease Functional. Biochemistry 2017; 56:2907-2920. [DOI: 10.1021/acs.biochem.7b00139] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Rajeswari Appadurai
- Department of Biotechnology,
Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600 036, India
| | - Sanjib Senapati
- Department of Biotechnology,
Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600 036, India
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31
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Su J, Liu X, Zhang S, Yan F, Zhang Q, Chen J. A computational insight into binding modes of inhibitors XD29, XD35, and XD28 to bromodomain-containing protein 4 based on molecular dynamics simulations. J Biomol Struct Dyn 2017; 36:1212-1224. [DOI: 10.1080/07391102.2017.1317666] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Jing Su
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China
| | - Xinguo Liu
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China
| | - Shaolong Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China
| | - Fangfang Yan
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China
| | - Qinggang Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China
| | - Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan, 250357, China
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32
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Shi S, Zhang S, Zhang Q. Insight into binding mechanisms of inhibitors MKP56, MKP73, MKP86, and MKP97 to HIV-1 protease by using molecular dynamics simulation. J Biomol Struct Dyn 2017; 36:981-992. [PMID: 28279118 DOI: 10.1080/07391102.2017.1305296] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
HIV-1 protease (PR) has been a significant target for design of potent inhibitors curing acquired immunodeficiency syndrome. Molecular dynamics simulations coupled with molecular mechanics Poisson-Boltzmann surface area method were performed to study interaction modes of four inhibitors MKP56, MKP73, MKP86, and MKP97 with PR. The results suggest that the main force controlling interactions of inhibitors with PR should be contributed by van der Waals interactions between inhibitors and PR. The cross-correlation analyses based on MD trajectories show that inhibitor binding produces significant effect on the flap dynamics of PR. Hydrogen bond analyses indicate that inhibitors can form stable hydrogen bonding interactions with the residues from the catalytic strands of PR. The contributions of separate residues to inhibitor bindings are evaluated by using residue-based free energy decomposition method and the results demonstrate that the CH-π and CH-CH interactions between the hydrophobic groups of inhibitors with residues drive the associations of inhibitors with PR. We expect that this study can provide a significant theoretical aid for design of potent inhibitors targeting PR.
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Affiliation(s)
- Shuhua Shi
- a School of Science , Shandong Jianzhu University , Jinan 250101 , China
| | - Shaolong Zhang
- b College of Physics and Electronics , Shandong Normal University , Jinan 250014 , China
| | - Qinggang Zhang
- b College of Physics and Electronics , Shandong Normal University , Jinan 250014 , China
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33
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Chen J. Functional roles of magnesium binding to extracellular signal-regulated kinase 2 explored by molecular dynamics simulations and principal component analysis. J Biomol Struct Dyn 2017; 36:351-361. [PMID: 28030988 DOI: 10.1080/07391102.2016.1277783] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Molecular dynamics (MD) simulations coupled with principal component (PC) analysis were carried out to study functional roles of Mg2+ binding to extracellular signal-regulated kinase 2 (ERK2). The results suggest that Mg2+ binding heavily decreases eigenvalue of the first principal component and totally inhibits motion strength of ERK2, which favors stabilization of ERK2 structure. Binding free energy predictions indicate that Mg2+ binding produces an important effect on binding ability of adenosine triphosphate (ATP) to ERK2 and strengthens the ATP binding. The calculations of residue-based free energy decomposition show that lack of Mg2+ weakens interactions between the hydrophobic rings of ATP and five residues I29, V37, A50, L105, and L154. Hydrogen bond analyses also prove that Mg2+ binding increases occupancies of hydrogen bonds formed between ATP and residues K52, Q103, D104, and M106. We expect that this study can provide a significant theoretical hint for designs of anticancer drugs targeting ERK2.
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Affiliation(s)
- Jianzhong Chen
- a School of Science, Shandong Jiaotong University , Jinan 250357 , China
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34
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Yang LQ, Sang P, Zhang RP, Liu SQ. Substrate-induced changes in dynamics and molecular motions of cuticle-degrading serine protease PL646: a molecular dynamics study. RSC Adv 2017. [DOI: 10.1039/c7ra07797a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Cuticle-degrading serine proteases secreted by nematophagous fungi can degrade the nematode cuticle during the infection processes.
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Affiliation(s)
- Li-Quan Yang
- College of Agriculture and Biological Science
- Dali University
- Dali
- P. R. China
- Collaborative Innovation Center for Biodiversity and Conservation in the Three Parallel Rivers Region of China
| | - Peng Sang
- College of Agriculture and Biological Science
- Dali University
- Dali
- P. R. China
- Collaborative Innovation Center for Biodiversity and Conservation in the Three Parallel Rivers Region of China
| | - Ruo-Peng Zhang
- Department of Reproductive Medicine
- The First Affiliated Hospital of Dali University
- Dali
- P. R. China
| | - Shu-Qun Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan
- Yunnan University
- Kunming
- P. R. China
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35
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Chen J, Wang J, Zhu W. Mutation L1196M-induced conformational changes and the drug resistant mechanism of anaplastic lymphoma kinase studied by free energy perturbation and umbrella sampling. Phys Chem Chem Phys 2017; 19:30239-30248. [DOI: 10.1039/c7cp05418a] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Anaplastic lymphoma kinase (ALK) has been regarded as a promising drug target in the treatment of tumors and the mutation L1196M induces different levels of drug resistance toward the existing inhibitors.
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Affiliation(s)
- Jianzhong Chen
- School of Science, Shandong Jiaotong University
- Jinan
- China
| | - Jinan Wang
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences
- Shanghai
- China
| | - Weiliang Zhu
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences
- Shanghai
- China
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36
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Molecular Mechanism and Energy Basis of Conformational Diversity of Antibody SPE7 Revealed by Molecular Dynamics Simulation and Principal Component Analysis. Sci Rep 2016; 6:36900. [PMID: 27830740 PMCID: PMC5103278 DOI: 10.1038/srep36900] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 10/21/2016] [Indexed: 01/12/2023] Open
Abstract
More and more researchers are interested in and focused on how a limited repertoire of antibodies can bind and correspondingly protect against an almost limitless diversity of invading antigens. In this work, a series of 200-ns molecular dynamics (MD) simulations followed by principal component (PC) analysis and free energy calculations were performed to probe potential mechanism of conformational diversity of antibody SPE7. The results show that the motion direction of loops H3 and L3 is different relative to each other, implying that a big structural difference exists between these two loops. The calculated energy landscapes suggest that the changes in the backbone angles ψ and φ of H-Y101 and H-Y105 provide significant contributions to the conformational diversity of SPE7. The dihedral angle analyses based on MD trajectories show that the side-chain conformational changes of several key residues H-W33, H-Y105, L-Y34 and L-W93 around binding site of SPE7 play a key role in the conformational diversity of SPE7, which gives a reasonable explanation for potential mechanism of cross-reactivity of single antibody toward multiple antigens.
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37
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Fast and accurate determination of the relative binding affinities of small compounds to HIV-1 protease using non-equilibrium work. J Comput Chem 2016; 37:2734-2742. [DOI: 10.1002/jcc.24502] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 08/29/2016] [Accepted: 09/06/2016] [Indexed: 02/06/2023]
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