1
|
Kiba Y, Tanikawa T, Hayashi T, Yokogawa T, Sano A, Suzuki R, Kitamura M. Inhibitory effects of senkyuchachosan on SARS-CoV-2 papain-like protease activity in vitro. J Nat Med 2024; 78:784-791. [PMID: 38512650 DOI: 10.1007/s11418-024-01788-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 02/02/2024] [Indexed: 03/23/2024]
Abstract
Papain-like protease (PLpro) enzyme plays a vital role in viral replication as it breaks down polyproteins and disrupts the host's immune response. There are few reports on Kampo formulas that focus on PLpro activity. In this study, we evaluated the inhibitory effects of senkyuchachosan, a traditional Japanese medicine, on PLpro of SARS-CoV-2, the virus responsible for causing COVID-19. We purified the PLpro enzyme and conducted in vitro enzymatic assays using specific substrates. Among the nine crude drugs present in senkyuchachosan, four (Cyperi Rhizoma, Schizonepetae Spica, Menthae Herba, and Camelliae sinensis Folium [CsF]) strongly inhibited PLpro activity. CsF, derived from Camellia sinensis (green tea), contains polyphenols, including catechins and tannins. To confirm that the PLpro inhibitory effects of senkyuchachosan predominantly stem from tannins, the tannins were removed from the decoction using polyvinylpolypyrrolidone (PVPP). The inhibitory effect of senkyuchachosan on PLpro activity was reduced by the removal of PVPP. In addition, the tannin fraction obtained from the CsF extracts showed significant PLpro inhibitory effects. These findings lay the groundwork for the potential development of therapeutic agents that target SARS-CoV-2 infection by intervening in proteolytic cleavage of the virus.
Collapse
Affiliation(s)
- Yuka Kiba
- School of Pharmacy, Faculty of Pharmacy and Pharmaceutical Sciences, Josai University, 1-1, Keyakidai, Sakado, Saitama, 350-0295, Japan
| | - Takashi Tanikawa
- School of Pharmacy, Faculty of Pharmacy and Pharmaceutical Sciences, Josai University, 1-1, Keyakidai, Sakado, Saitama, 350-0295, Japan
| | - Tsuyoshi Hayashi
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Takami Yokogawa
- School of Pharmacy, Faculty of Pharmacy and Pharmaceutical Sciences, Josai University, 1-1, Keyakidai, Sakado, Saitama, 350-0295, Japan
| | - Aiko Sano
- Department of Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences, Josai University, 1-1, Keyakidai, Sakado, Saitama, 350-0295, Japan
| | - Ryuichiro Suzuki
- Department of Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences, Josai University, 1-1, Keyakidai, Sakado, Saitama, 350-0295, Japan
| | - Masashi Kitamura
- School of Pharmacy, Faculty of Pharmacy and Pharmaceutical Sciences, Josai University, 1-1, Keyakidai, Sakado, Saitama, 350-0295, Japan.
| |
Collapse
|
2
|
Shahzadi Z, Yousaf Z, Anjum I, Bilal M, Yasin H, Aftab A, Booker A, Ullah R, Bari A. Network pharmacology and molecular docking: combined computational approaches to explore the antihypertensive potential of Fabaceae species. BIORESOUR BIOPROCESS 2024; 11:53. [PMID: 38767701 DOI: 10.1186/s40643-024-00764-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 04/26/2024] [Indexed: 05/22/2024] Open
Abstract
Hypertension is a major global public health issue, affecting quarter of adults worldwide. Numerous synthetic drugs are available for treating hypertension; however, they often come with a higher risk of side effects and long-term therapy. Modern formulations with active phytoconstituents are gaining popularity, addressing some of these issues. This study aims to discover novel antihypertensive compounds in Cassia fistula, Senna alexandrina, and Cassia occidentalis from family Fabaceae and understand their interaction mechanism with hypertension targeted genes, using network pharmacology and molecular docking. Total 414 compounds were identified; initial screening was conducted based on their pharmacokinetic and ADMET properties, with a particular emphasis on adherence to Lipinski's rules. 6 compounds, namely Germichrysone, Benzeneacetic acid, Flavan-3-ol, 5,7,3',4'-Tetrahydroxy-6, 8-dimethoxyflavon, Dihydrokaempferol, and Epiafzelechin, were identified as effective agents. Most of the compounds found non-toxic against various indicators with greater bioactivity score. 161 common targets were obtained against these compounds and hypertension followed by compound-target network construction and protein-protein interaction, which showed their role in diverse biological system. Top hub genes identified were TLR4, MMP9, MAPK14, AKT1, VEGFA and HSP90AA1 with their respective associates. Higher binding affinities was found with three compounds Dihydrokaempferol, Flavan-3-ol and Germichrysone, -7.1, -9.0 and -8.0 kcal/mol, respectively. The MD simulation results validate the structural flexibility of two complexes Flavan-MMP9 and Germich-TLR4 based on no. of hydrogen bonds, root mean square deviations and interaction energies. This study concluded that C. fistula (Dihydrokaempferol, Flavan-3-ol) and C. occidentalis (Germichrysone) have potential therapeutic active constituents to treat hypertension and in future novel drug formulation.
Collapse
Affiliation(s)
- Zainab Shahzadi
- Department of Botany, Lahore College for Women University, Lahore, Pakistan
| | - Zubaida Yousaf
- Department of Botany, Lahore College for Women University, Lahore, Pakistan.
| | - Irfan Anjum
- Department of Basic Medical Sciences, Shifa College of Pharmaceutical Sciences, Shifa Tameer-e-Millat University, Islamabad, Pakistan
| | - Muhammad Bilal
- Centers for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Hamna Yasin
- Department of Botany, Lahore College for Women University, Lahore, Pakistan
| | - Arusa Aftab
- Department of Botany, Lahore College for Women University, Lahore, Pakistan
| | - Anthony Booker
- Research Centre for Optimal Health, School of Life Sciences, College of Liberal Arts and Sciences, University of Westminster, 115 New Cavendish Street, London, W1W 6UW, UK.
- Research Group 'Pharmacognosy and Phytotherapy', UCL School of Pharmacy, Univ. London, 29 - 39 Brunswick Sq., London, WC1N 1AX, UK.
| | - Riaz Ullah
- Department of Pharmacognosy, College of Pharmacy King, Saud University, Riyadh, Saudi Arabia
| | - Ahmed Bari
- Department of Pharmaceutical Chemistry, College of Pharmacy King, Saud University, Riyadh, Saudi Arabia
| |
Collapse
|
3
|
Gupta A, Purohit R. Identification of potent BRD4-BD1 inhibitors using classical and steered molecular dynamics based free energy analysis. J Cell Biochem 2024; 125:e30532. [PMID: 38317535 DOI: 10.1002/jcb.30532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/08/2024] [Accepted: 01/26/2024] [Indexed: 02/07/2024]
Abstract
In the present work a combination of traditional and steered molecular dynamics based techniques were employed to identify potential inhibitors against the human BRD4 protein (BRD4- BD1); an established drug target for multiple illnesses including various malignancies. Quinoline derivatives that were synthesized in-house were tested for their potential as new BRD4-BD1 inhibitors. Initially molecular docking experiments were performed to determine the binding poses of BRD4-BD1 inhibitors. To learn more about the thermodynamics of inhibitor binding to the BRD4-BD1 active site, the Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) free energy calculations were conducted afterwards. The findings of the MM-PBSA analysis were further reinforced by performing steered umbrella sampling simulations which revealed crucial details about the binding/unbinding process of the most potent quinoline derivatives at the BRD4-BD1 active site. We report a novel quinoline derivative which can be developed into a fully functional BRD4-BD1 inhibitor after experimental validation. The identified compound (4 g) shows better properties than the standard BRD4-BD1 inhibitors considered in the study. The study also highlights the crucial role of Gln78, Phe79, Trp81, Pro82, Phe83, Gln84, Gln85, Val87, Leu92, Leu94, Tyr97, Met105, Cys136, Asn140, Ile146 and Met149 in inhibitor binding. The study provides a possible lead candidate and key amino acids involved in inhibitor recognition and binding at the active site of BRD4-BD1 protein. The findings might be of significance to medicinal chemists involved in the development of potent BRD4-BD1 inhibitors.
Collapse
Affiliation(s)
- Ashish Gupta
- Structural Bioinformatics Lab, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, India
| | - Rituraj Purohit
- Structural Bioinformatics Lab, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, India
| |
Collapse
|
4
|
Yang ZS, Li TS, Huang YS, Chang CC, Chien CM. Targeting the receptor binding domain and heparan sulfate binding for antiviral drug development against SARS-CoV-2 variants. Sci Rep 2024; 14:2753. [PMID: 38307890 PMCID: PMC10837157 DOI: 10.1038/s41598-024-53111-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 01/27/2024] [Indexed: 02/04/2024] Open
Abstract
The emergence of SARS-CoV-2 variants diminished the efficacy of current antiviral drugs and vaccines. Hence, identifying highly conserved sequences and potentially druggable pockets for drug development was a promising strategy against SARS-CoV-2 variants. In viral infection, the receptor-binding domain (RBD) proteins are essential in binding to the host receptor. Others, Heparan sulfate (HS), widely distributed on the surface of host cells, is thought to play a central role in the viral infection cycle of SARS-CoV-2. Therefore, it might be a reasonable strategy for antiviral drug design to interfere with the RBD in the HS binding site. In this study, we used computational approaches to analyze multiple sequences of coronaviruses and reveal important information about the binding of HS to RBD in the SARS-CoV-2 spike protein. Our results showed that the potential hot-spots, including R454 and E471, in RBD, exhibited strong interactions in the HS-RBD binding region. Therefore, we screened different compounds in the natural product database towards these hot-spots to find potential antiviral candidates using LibDock, Autodock vina and furthermore applying the MD simulation in AMBER20. The results showed three potential natural compounds, including Acetoside (ACE), Hyperoside (HYP), and Isoquercitrin (ISO), had a strong affinity to the RBD. Our results demonstrate a feasible approach to identify potential antiviral agents by evaluating the binding interaction between viral glycoproteins and host receptors. The present study provided the applications of the structure-based computational approach for designing and developing of new antiviral drugs against SARS-CoV-2 variants.
Collapse
Affiliation(s)
- Zi-Sin Yang
- Department of Medical Sciences Industry, College of Health Sciences, Chang Jung Christian University, Tainan, 711, Taiwan
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Tzong-Shiun Li
- Graduate Institute of Biomedical Engineering, National Chung Hsing University, Taichung, 402, Taiwan
- Department of Plastic Surgery, Chang Bing Show Chwan Memorial Hospital, Changhua, 500, Taiwan
| | - Yu-Sung Huang
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Cheng-Chung Chang
- Graduate Institute of Biomedical Engineering, National Chung Hsing University, Taichung, 402, Taiwan
| | - Ching-Ming Chien
- Department of Medical Sciences Industry, College of Health Sciences, Chang Jung Christian University, Tainan, 711, Taiwan.
| |
Collapse
|
5
|
Annan A, Raiss N, Lemrabet S, Elomari N, Elmir EH, Filali-Maltouf A, Medraoui L, Oumzil H. Proposal of pharmacophore model for HIV reverse transcriptase inhibitors: Combined mutational effect analysis, molecular dynamics, molecular docking and pharmacophore modeling study. Int J Immunopathol Pharmacol 2024; 38:3946320241231465. [PMID: 38296818 PMCID: PMC10832406 DOI: 10.1177/03946320241231465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 01/13/2024] [Indexed: 02/02/2024] Open
Abstract
OBJECTIVES Antiretroviral therapy (ART) efficacy is jeopardized by the emergence of drug resistance mutations in HIV, compromising treatment effectiveness. This study aims to propose novel analogs of Effavirenz (EFV) as potential direct inhibitors of HIV reverse transcriptase, employing computer-aided drug design methodologies. METHODS Three key approaches were applied: a mutational profile study, molecular dynamics simulations, and pharmacophore development. The impact of mutations on the stability, flexibility, function, and affinity of target proteins, especially those associated with NRTI, was assessed. Molecular dynamics analysis identified G190E as a mutation significantly altering protein properties, potentially leading to therapeutic failure. Comparative analysis revealed that among six first-line antiretroviral drugs, EFV exhibited notably low affinity with viral reverse transcriptase, further reduced by the G190E mutation. Subsequently, a search for EFV-similar inhibitors yielded 12 promising molecules based on their affinity, forming the basis for generating a pharmacophore model. RESULTS Mutational analysis pinpointed G190E as a crucial mutation impacting protein properties, potentially undermining therapeutic efficacy. EFV demonstrated diminished affinity with viral reverse transcriptase, exacerbated by the G190E mutation. The search for EFV analogs identified 12 high-affinity molecules, culminating in a pharmacophore model elucidating key structural features crucial for potent inhibition. CONCLUSION This study underscores the significance of EFV analogs as potential inhibitors of HIV reverse transcriptase. The findings highlight the impact of mutations on drug efficacy, particularly the detrimental effect of G190E. The generated pharmacophore model serves as a pivotal reference for future drug development efforts targeting HIV, providing essential structural insights for the design of potent inhibitors based on EFV analogs identified in vitro.
Collapse
Affiliation(s)
- Azzeddine Annan
- Research Center of Plant and Microbial Biotechnologies, Biodiversity and Environment, Faculty of Sciences, Mohammed V University, Rabat, Morocco
- Virology Department, National Reference Laboratory for HIV, Institute National of Hygiene, Rabat, Morocco
| | - Noureddine Raiss
- Research Center of Plant and Microbial Biotechnologies, Biodiversity and Environment, Faculty of Sciences, Mohammed V University, Rabat, Morocco
- Virology Department, National Reference Laboratory for HIV, Institute National of Hygiene, Rabat, Morocco
| | - Sanae Lemrabet
- Virology Department, National Reference Laboratory for HIV, Institute National of Hygiene, Rabat, Morocco
| | - Nezha Elomari
- Virology Department, National Reference Laboratory for HIV, Institute National of Hygiene, Rabat, Morocco
| | - El Harti Elmir
- Virology Department, National Reference Laboratory for HIV, Institute National of Hygiene, Rabat, Morocco
| | - Abdelkarim Filali-Maltouf
- Research Center of Plant and Microbial Biotechnologies, Biodiversity and Environment, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Leila Medraoui
- Research Center of Plant and Microbial Biotechnologies, Biodiversity and Environment, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Hicham Oumzil
- Virology Department, National Reference Laboratory for HIV, Institute National of Hygiene, Rabat, Morocco
- Pedagogy and Research Unit of Microbiology, and Genomic Center of Human Pathologies, School of Medicine and Pharmacy, Mohamed V University, Rabat, Morocco
| |
Collapse
|
6
|
Temre MK, Devi B, Singh VK, Goel Y, Yadav S, Pandey SK, Kumar R, Kumar A, Singh SM. Molecular characterization of glutor-GLUT interaction and prediction of glutor's drug-likeness: implications for its utility as an antineoplastic agent. J Biomol Struct Dyn 2023; 41:11262-11273. [PMID: 36571488 DOI: 10.1080/07391102.2022.2161010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 12/15/2022] [Indexed: 12/27/2022]
Abstract
Recent experimental evidence from our and other laboratories has strongly indicated that glutor, a piperazine-2-one derivative, which is a pan-GLUT inhibitor, displays a promising antineoplastic action by hampering glucose uptake owing to its ability to inhibit GLUT1 and GLUT3, which are overexpressed in neoplastic cells. However, the molecular mechanism(s) of the inhibiting action of glutor has remained elusive. Thus, for optimal utilization of the antineoplastic potential of glutor, it is essential to decipher the precise mechanism(s) of its interaction with GLUTs. Therefore, the present investigation was carried out to understand the molecular mechanism(s) of the binding of glutor to GLUT1 and GLUT3 in silico. This study suggests that glutor can effectively bind to GLUTs at the reported binding site. Moreover, the docking of glutor to GLUT was stabilised by several contacts between these two partners as shown by the 200 ns long molecular dynamic simulation carried out using Gromacs, indicating the formation of a stable complex. Moreover, glutor was found to possess all characteristics conducive to its drug-likeness. Hence, these observations suggest that glutor has the potential to be used in antineoplastic therapeutic applications.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Mithlesh Kumar Temre
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Bharti Devi
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (BHU), Varanasi, India
| | - Vinay Kumar Singh
- Centre for Bioinformatics, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Yugal Goel
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Saveg Yadav
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Shrish Kumar Pandey
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Rajnish Kumar
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (BHU), Varanasi, India
| | - Ajay Kumar
- Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Sukh Mahendra Singh
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
| |
Collapse
|
7
|
Deshpande N S, Dwivedi PSR, Revanasiddappa BC. Virtual screening, pharmacokinetics & MD simulation study of active phytoconstituents of Ficus Carica Linn. against PPAR-γ in diabetes mellitus. J Biomol Struct Dyn 2023:1-17. [PMID: 37948295 DOI: 10.1080/07391102.2023.2279286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 10/30/2023] [Indexed: 11/12/2023]
Abstract
F. carica is a small tree and commonly used as a traditional medicine against several disorders. Diabetes is currently treated with insulin and oral hypoglycemic medicines such as sulphonyl urea derivatives, bigunides, thiazolidinediones and alpha-glucosidase inhibitors. Peroxisome proliferator-activated receptor gamma (PPAR-γ) agonists were found to be very much beneficial in the management of diabetes by inhibiting hepatic gluconeogenesis. The aim of this study is to evaluate the bioactive phytoconstituents from Ficus carica Linn. against the target PPAR-γ agonist by in silico docking approach. We investigated 68 phytoconstituents as potential inhibitors of PPAR-γ agonists and the top 24 phytoconstituents were further selected for molecular docking studies. Drug ability, side effects, and ADMET analysis were determined by using MolSoft, toxtree freeware, and ADMET SAR web server, respectively. The phytoconstituents were docked with the target PPAR-γ (PDB ID: 4Y29, 1.98 Å) receptor. Quercetin-3-o-rutinoside possessed the highest G score -14.22 kcal/mol, followed by Angelicin with a G score of -13.56 kcal/mol. All the other phytoconstituents displayed good pharmacokinetic and toxicological parameters with values within the permissible limits. The ligand-protein interaction was calculated by molecular dynamic (MD) simulation study. Subsequently, the binding free energy of the Quercetin-3-o-rutinosideand Pioglitazone complex was calculated using MMPBSA analysis. The results indicated that some of the phytoconstituents from Ficus carica have potency as an anti-diabetic agents. So, these bioactive phytoconstituents like Quercetin-3-o-glucoside, 5-O-caffeoylquinic acids may act as a good agonist for PPAR-γ.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Shridhar Deshpande N
- Department of Pharmaceutical Chemistry, NGSM Institute of Pharmaceutical Sciences (NGSMIPS) Nitte (Deemed to Be University, Mangalore, Karnataka, India
| | - Prarambh S R Dwivedi
- Department of Pharmacology, NGSM Institute of Pharmaceutical Sciences (NGSMIPS) Nitte (Deemed to Be University), Mangalore, Karnataka, India
| | - B C Revanasiddappa
- Department of Pharmaceutical Chemistry, NGSM Institute of Pharmaceutical Sciences (NGSMIPS) Nitte (Deemed to Be University, Mangalore, Karnataka, India
| |
Collapse
|
8
|
Pawar A, Konwar C, Jha P, Kant R, Chopra M, Chaudhry U, Saluja D. Bactericidal activity of esculetin is associated with impaired cell wall synthesis by targeting glutamate racemase of Neisseria gonorrhoeae. Mol Divers 2023:10.1007/s11030-023-10745-0. [PMID: 37880544 DOI: 10.1007/s11030-023-10745-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 10/08/2023] [Indexed: 10/27/2023]
Abstract
Neisseria gonorrhoeae (NG), the causative organism of gonorrhea, has been classified by the World Health Organization as 'Priority' two organism owing to its increased resistance to antibiotics and even failure of recommended dual therapy with ceftriaxone and azithromycin. As a result, the general and reproductive health of infected individuals is severely compromised. The imminent public health catastrophe of antimicrobial-resistant gonococci cannot be understated, as t he of severe complications and sequelae of infection are not only increasing but their treatment has also become more expensive. Tenacious attempts are underway to discover novel drug targets as well as new drugs to fight against NG. Therefore, a considerable number of phytochemicals have been tested for their remedial intercession via targeting bacterial proteins. The MurI gene encodes for an enzyme called glutamate racemase (MurI) that is primarily involved in peptidoglycan (PG) biosynthesis and is specific to the bacterial kingdom and hence can be exploited as a potential drug target for the treatment of bacterial diseases. Accordingly, diverse families of phytochemicals were screened in silico for their binding affinity with N. Gonorrhoeae MurI (NG-MurI) protein. Esculetin, one of the shortlisted compounds, was evaluated for its functional, structural, and anti-bacterial activity. Treatment with esculetin resulted in growth inhibition, cell wall damage, and altered permeability as revealed by fluorescence and electron microscopy. Furthermore, esculetin inhibited the racemization activity of recombinant, purified NG-MurI protein, one of the enzymes required for peptidoglycan biosynthesis. Our results suggest that esculetin could be further explored as a lead compound for developing new drug molecules against multidrug-resistant strains.
Collapse
Affiliation(s)
- Alka Pawar
- Dr. B. R. Ambedkar Center for Biomedical Research, Delhi School of Public Health, IoE, University of Delhi, Delhi, 110007, India
| | - Chandrika Konwar
- Dr. B. R. Ambedkar Center for Biomedical Research, Delhi School of Public Health, IoE, University of Delhi, Delhi, 110007, India
| | - Prakash Jha
- Dr. B. R. Ambedkar Center for Biomedical Research, Delhi School of Public Health, IoE, University of Delhi, Delhi, 110007, India
| | - Ravi Kant
- Dr. B. R. Ambedkar Center for Biomedical Research, Delhi School of Public Health, IoE, University of Delhi, Delhi, 110007, India
| | - Madhu Chopra
- Dr. B. R. Ambedkar Center for Biomedical Research, Delhi School of Public Health, IoE, University of Delhi, Delhi, 110007, India
| | - Uma Chaudhry
- Bhaskaracharya College of Applied Sciences, University of Delhi, Delhi, 110075, India
| | - Daman Saluja
- Dr. B. R. Ambedkar Center for Biomedical Research, Delhi School of Public Health, IoE, University of Delhi, Delhi, 110007, India.
- Delhi School of Public Health, IoE, University of Delhi, Delhi, 110007, India.
| |
Collapse
|
9
|
Viskupicova J, Rezbarikova P, Kovacikova L, Kandarova H, Majekova M. Inhibitors of SARS-CoV-2 main protease: Biological efficacy and toxicity aspects. Toxicol In Vitro 2023; 92:105640. [PMID: 37419426 DOI: 10.1016/j.tiv.2023.105640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/19/2023] [Accepted: 06/30/2023] [Indexed: 07/09/2023]
Abstract
The emergence of the highly contagious respiratory disease, COVID-19, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become a significant global public health concern. To combat this virus, researchers have focused on developing antiviral strategies that target specific viral components, such as the main protease (Mpro), which plays a crucial role in SARS-CoV-2 replication. While many compounds have been identified as potent inhibitors of Mpro, only a few have been translated into clinical use due to the potential risk-benefit trade-offs. Development of systemic inflammatory response and bacterial co-infection in patients belong to severe, frequent complications of COVID-19. In this context, we analysed available data on the anti-inflammatory and antibacterial activities of the SARS-CoV-2 Mpro inhibitors for possible implementation in the treatment of complicated and long COVID-19 cases. Synthetic feasibility and ADME properties were calculated and included for better characterisation of the compounds' predicted toxicity. Analysis of the collected data resulted in several clusters pointing to the most prospective compounds for further study and design. The complete tables with collected data are attached in Supplementary material for use by other researchers.
Collapse
Affiliation(s)
- Jana Viskupicova
- Centre of Experimental Medicine, Slovak Academy of Sciences, Bratislava, Slovakia
| | | | - Lucia Kovacikova
- Centre of Experimental Medicine, Slovak Academy of Sciences, Bratislava, Slovakia; Department of Organic Chemistry, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Helena Kandarova
- Centre of Experimental Medicine, Slovak Academy of Sciences, Bratislava, Slovakia; Institute of Biochemistry and Microbiology, Faculty of Chemical and Food Technology, Slovak University of Technology, Bratislava, Slovakia
| | - Magdalena Majekova
- Centre of Experimental Medicine, Slovak Academy of Sciences, Bratislava, Slovakia.
| |
Collapse
|
10
|
Vyshnavi AM H, Sankaran S, Namboori PK K, Venkidasamy B, Hirad AH, Alarfaj AA, Vinayagam R. In Silico Analysis of the Effect of Hydrastis canadensis on Controlling Breast Cancer. Medicina (Kaunas) 2023; 59:1412. [PMID: 37629702 PMCID: PMC10456556 DOI: 10.3390/medicina59081412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 07/19/2023] [Accepted: 07/25/2023] [Indexed: 08/27/2023]
Abstract
Background and Objectives: Breast cancer is a significant type of cancer among women worldwide. Studies have reported the anti-carcinogenic activity of Hydrastis Canadensis (Goldenseal) in cancer cell lines. Hydrastis Canadensis could help eliminate toxic substances due to its anti-cancer, anti-inflammatory, and other properties. The design phase includes the identification of potential and effective molecules through modern computational techniques. Objective: This work aims to study Hydrastis Canadensis's effect in controlling hormone-independent breast cancer through in-silico analysis. Materials and Methods: The preliminary screening of reported phytochemicals includes biomolecular networking. Identifying functionally relevant phytochemicals and the respective target mutations/genes leads to selecting 3D proteins of the desired mutations being considered the target. Interaction studies have been conducted using docking. The kinetic and thermodynamic stability of complexes was studied through molecular dynamic simulation and MM-PBSA/GBSA analysis. Pharmacodynamic and pharmacokinetic features have been predicted. The mechanism-wise screening, functional enrichment, and interactional studies suggest that canadaline and Riboflavin effectively interact with the target proteins. Results: Hydrastis Canadensis has been identified as the effective formulation containing all these constituents. The phytoconstituents; Riboflavin and Canadensis showed good interaction with the targets of hormone-independent breast cancer. The complexes were found to be kinetically and thermodynamically stable. Conclusions: Hydrastis Canadensis has been identified as effective in controlling 'hormone-independent or basal-like breast cancer' followed by 'hormone-dependent breast cancer: Luminal A' and Luminal B.
Collapse
Affiliation(s)
- Hima Vyshnavi AM
- Computational Chemistry Group (CCG), Amrita School of Engineering, Amrita Vishwa Vidyapeetham, Coimbatore 641112, India;
| | - Sathianarayanan Sankaran
- Department of Pharmaceutical Chemistry, NGSM Institute of Pharmaceutical Sciences, Nitte (Deemed to be University), Deralakatte, Mangaluru 575018, India;
| | - Krishnan Namboori PK
- Computational Chemistry Group (CCG), Amrita School of Engineering, Amrita Vishwa Vidyapeetham, Coimbatore 641112, India;
| | - Baskar Venkidasamy
- Department of Oral & Maxillofacial Surgery, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai 600077, India;
| | - Abdurahman Hajinur Hirad
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia; (A.H.H.); (A.A.A.)
| | - Abdullah A. Alarfaj
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia; (A.H.H.); (A.A.A.)
| | - Ramachandran Vinayagam
- Department of Biotechnology, Institute of Biotechnology, College of Life and Applied Sciences, Yeungnam University, 280 Daehak-Ro, Gyeongsan 38541, Gyeongbuk, Republic of Korea
| |
Collapse
|
11
|
Oyedele AQK, Ogunlana AT, Boyenle ID, Adeyemi AO, Rita TO, Adelusi TI, Abdul-Hammed M, Elegbeleye OE, Odunitan TT. Docking covalent targets for drug discovery: stimulating the computer-aided drug design community of possible pitfalls and erroneous practices. Mol Divers 2023; 27:1879-1903. [PMID: 36057867 PMCID: PMC9441019 DOI: 10.1007/s11030-022-10523-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 08/26/2022] [Indexed: 01/18/2023]
Abstract
The continuous approval of covalent drugs in recent years for the treatment of diseases has led to an increased search for covalent agents by medicinal chemists and computational scientists worldwide. In the computational parlance, molecular docking which is a popular tool to investigate the interaction of a ligand and a protein target, does not account for the formation of covalent bond, and the increasing application of these conventional programs to covalent targets in early drug discovery practice is a matter of utmost concern. Thus, in this comprehensive review, we sought to educate the docking community about the realization of covalent docking and the existence of suitable programs to make their future virtual-screening events on covalent targets worthwhile and scientifically rational. More interestingly, we went beyond the classical description of the functionality of covalent-docking programs down to selecting the 'best' program to consult with during a virtual-screening campaign based on receptor class and covalent warhead chemistry. In addition, we made a highlight on how covalent docking could be achieved using random conventional docking software. And lastly, we raised an alert on the growing erroneous molecular docking practices with covalent targets. Our aim is to guide scientists in the rational docking pursuit when dealing with covalent targets, as this will reduce false-positive results and also increase the reliability of their work for translational research.
Collapse
Affiliation(s)
- Abdul-Quddus Kehinde Oyedele
- Computational Biology/Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
- Department of Chemistry, University of New Haven, West Haven, CT, USA
| | - Abdeen Tunde Ogunlana
- Computational Biology/Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
| | - Ibrahim Damilare Boyenle
- Computational Biology/Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Nigeria.
- Department of Chemistry and Biochemsitry, University of Maryland, Maryland, USA.
- College of Health Sciences, Crescent University, Abeokuta, Nigeria.
| | | | - Temionu Oluwakemi Rita
- Department of Medical Laboratory Technology, Lagos State College of Health, Lagos, Nigeria
| | - Temitope Isaac Adelusi
- Computational Biology/Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
| | - Misbaudeen Abdul-Hammed
- Department of Pure and Applied Chemistry, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
| | - Oluwabamise Emmanuel Elegbeleye
- Computational Biology/Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
| | - Tope Tunji Odunitan
- Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
| |
Collapse
|
12
|
Lawal B, Kuo YC, Onikanni SA, Chen YF, Abdulrasheed-Adeleke T, Fadaka AO, Olugbodi JO, Lukman HY, Olawale F, Mahmoud MH, Batiha GES, Wu ATH, Huang HS. Computational identification of novel signature of T2DM-induced nephropathy and therapeutic bioactive compounds from Azanza garckeana. Am J Transl Res 2023; 15:4504-4520. [PMID: 37560206 PMCID: PMC10408496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 05/30/2023] [Indexed: 08/11/2023]
Abstract
OBJECTIVES Diabetic nephropathy (DN) is one of the most prevalent secondary complications associated with diabetes mellitus. Decades of research have implicated multiple pathways in the etiology and pathophysiology of diabetic nephropathy. There has been no reliable predictive biomarkers for the onset or progression of DN and no successful treatments are available. METHODS In the present study, we explored the datasets of RNA sequencing data from patients with Type II diabetes mellitus (T2DM)-induced nephropathy to identify a novel gene signature. We explored the target bioactive compounds identified from Azanza garckeana, a medicinal plant commonly used by the traditional treatment of diabetes nephropathy. RESULTS Our analysis identified lymphotoxin beta (LTB), SRY-box transcription factor 4 (SOX4), SOX9, and WAP four-disulfide core domain protein 2 (WFDC2) as novel signatures of T2DM-induced nephropathy. Additional analysis revealed the pathological involvement of the signature in cell-cell adhesion, immune, and inflammatory responses during diabetic nephropathy. Molecular docking and dynamic simulation at 100 ns conducted studies revealed that among the three compounds, Terpinen-4-ol exhibited higher binding efficacies (binding energies (ΔG) = -3.9~5.5 kcal/mol) against the targets. The targets, SOX4, and SOX9 demonstrated higher druggability towards the three compounds. WFDC2 was the least attractive target for the compounds. CONCLUSION The present study was relevant in the diagnosis, prognosis, and treatment follow up of patients with diabetes induced nephropathy. The study provided an insight into the therapeutic application of the bioactive principles from Azanza garckeana. Continued follow-up invitro validations study are ongoing in our laboratory.
Collapse
Affiliation(s)
- Bashir Lawal
- UPMC Hillman Cancer Center, University of PittsburghPittsburgh, PA, USA
- Department of Pathology, University of PittsburghPittsburgh, PA 15213, USA
| | - Yu-Cheng Kuo
- Department of Pharmacology, School of Medicine, College of Medicine, Taipei Medical UniversityTaipei 11031, Taiwan
- School of Post-Baccalaureate Chinese Medicine, College of Chinese Medicine, China Medical UniversityTaichung 40402, Taiwan
| | - Sunday Amos Onikanni
- Department of Chemical Sciences, Biochemistry Unit, Afe-Babalola UniversityAdo-Ekiti, Ekiti State, Nigeria
- College of Medicine, Graduate Institute of Biomedical Sciences, China Medical UniversityTaiwan
| | - Yi-Fong Chen
- Division of Medicinal Products, Taiwan Food and Drug Administration, Ministry of Health and WelfareNo.161-2, Kunyang St., Nangang Dist., Taipei City 115209, Taiwan
| | | | - Adewale Oluwaseun Fadaka
- Department of Science and Innovation (DSI)/Mintek Nanotechnology Innovation Centre (NIC) Biolabels Research Node, Department of Biotechnology, University of the Western CapeBellville 7535, South Africa
| | | | - Halimat Yusuf Lukman
- Department of Chemical Sciences, Biochemistry Unit, College of Natural and Applied Sciences, Summit UniversityOffa, PMB 4412, Nigeria
| | - Femi Olawale
- Department of Biochemistry, School of Life Science, University of KwaZulu NatalDurban, South Africa
| | - Mohamed H Mahmoud
- Department of Biochemistry, College of Science, King Saud UniversityRiyadh, Saudi Arabia
| | - Gaber El-Saber Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicine, Damanhour UniversityDamanhour 22511, AlBeheira, Egypt
| | - Alexander TH Wu
- TMU Research Center of Cancer Translational Medicine, Taipei Medical UniversityTaipei 11031, Taiwan
- The Ph.D. Program of Translational Medicine, College of Medical Science and Technology, Taipei Medical UniversityTaipei 11031, Taiwan
- Clinical Research Center, Taipei Medical University Hospital, Taipei Medical UniversityTaipei 11031, Taiwan
- Graduate Institute of Medical Sciences, National Defense Medical CenterTaipei 114, Taiwan
| | - Hsu-Shan Huang
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, and Academia SinicaTaipei 11031, Taiwan
- Graduate Institute for Cancer Biology & Drug Discovery, College of Medical Science and Technology, Taipei Medical UniversityTaipei 11031, Taiwan
- Graduate Institute of Medical Sciences, National Defense Medical CentreTaipei 11490, Taiwan
- School of Pharmacy, National Defense Medical CentreTaipei 11490, Taiwan
- Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical UniversityTaipei 11031, Taiwan
| |
Collapse
|
13
|
Lawal B, Wu AT, Chen CH, T A G, Wu SY. Identification of INFG/STAT1/NOTCH3 as γ-Mangostin's potential targets for overcoming doxorubicin resistance and reducing cancer-associated fibroblasts in triple-negative breast cancer. Biomed Pharmacother 2023; 163:114800. [PMID: 37141739 DOI: 10.1016/j.biopha.2023.114800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/06/2023] Open
Abstract
Triple-negative breast cancer (TNBC) is a very aggressive subtype of breast cancer characterized by drug resistance and distant metastasis. Cancer stem cells (CSCs) are considered a major contributor to TNBC's drug resistance. Thus targeting and eliminating CSCs have been vigorously researched. However, the precise targetable molecular networks responsible for CSC genesis remain unclear; this conundrum is mainly due to the high heterogeneity of the TNBC tumor microenvironment (TME). The cancer-associated fibroblasts (CAFs) are one of the most abundant cellular components of the TME. Emerging studies indicate that CAFs facilitate TNBC's progression by establishing a pro-tumor TME. Hence, identifying the molecular networks involved in CAF transformation and CAF-associated oncogenesis are essential areas to be explored. Through a bioinformatics approach, we identified INFG/STAT1/NOTCH3 as a molecular link between CSCs and CAF. DOX-resistant TNBC cell lines showed increased expression of INFG/STAT1/NOTCH3 and CD44 and were associated with increased self-renewal ability and CAF-transformative ability. Downregulation of STAT1 significantly reduced the tumorigenic properties of MDA-MB-231 and -468 cells and their CAF-transforming potential. Our molecular docking analysis suggested that gamma mangostin (gMG), a xanthone, formed complexes with INFG/STAT1/NOTCH3 better than celecoxib. We then demonstrated that gMG treatment reduced the tumorigenic properties similarly observed in STAT1-knocked down conditions. Finally, we utilized a DOX-resistant TNBC tumoroid-bearing mouse model to demonstrate that gMG treatment significantly delayed tumor growth, reduced CAF generation, and improved DOX sensitivity. Further investigations are warranted for clinical translation.
Collapse
Affiliation(s)
- Bashir Lawal
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA; Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Alexander Th Wu
- TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei 11031, Taiwan; The Ph.D. Program of Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; Clinical Research Center, Taipei Medical University Hospital, Taipei Medical University, Taipei 11031, Taiwan; Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei 114, Taiwan
| | - Chien-Hsin Chen
- Department of Surgery, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan; Department of Colorectal Surgery, Wan Fang Hospital, Taipei Medical University, Taipei 11031, Taiwan
| | - George T A
- College of Medicine and Allied Health Sciences, University of Sierra Leone, Sierra Leone
| | - Szu-Yuan Wu
- Department of Food Nutrition and Health Biotechnology, College of Medical and Health Science, Asia University, Taichung, Taiwan; Department of Healthcare Administration, College of Medical and Health Science, Asia University, Taichung, Taiwan; Graduate Institute of Business Administration, College of Management, Fu Jen Catholic University, Taipei, Taiwan; Artificial Intelligence Development Centre, Fu Jen Catholic University, Taipei, Taiwan; Centre for Regional Anaesthesia and Pain Medicine, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan; Big Data Centre, Lo-Hsu Medical Foundation, Lotung Poh-Ai Hospital, Yilan, Taiwan; Division of Radiation Oncology, Lo-Hsu Medical Foundation, Lotung Poh-Ai Hospital, Yilan, Taiwan.
| |
Collapse
|
14
|
Wu J, Gao T, Guo H, Zhao L, Lv S, Lv J, Yao R, Yu Y, Ma F. Application of molecular dynamics simulation for exploring the roles of plant biomolecules in promoting environmental health. Sci Total Environ 2023; 869:161871. [PMID: 36708839 DOI: 10.1016/j.scitotenv.2023.161871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 01/23/2023] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
Understanding the dynamic changes of plant biomolecules is vital for exploring their mechanisms in the environment. Molecular dynamics (MD) simulation has been widely used to study structural evolution and corresponding properties of plant biomolecules at the microscopic scale. Here, this review (i) outlines structural properties of plant biomolecules, and the crucial role of MD simulation in advancing studies of the biomolecules; (ii) describes the development of MD simulation in plant biomolecules, determinants of simulation, and analysis parameters; (iii) introduces the applications of MD simulation in plant biomolecules, including the response of the biomolecules to multiple stresses, their roles in corrosive environments, and their contributions in improving environmental health; (iv) reviews techniques integrated with MD simulation, such as molecular biology, quantum mechanics, molecular docking, and machine learning modeling, which bridge gaps in MD simulation. Finally, we make suggestions on determination of force field types, investigation of plant biomolecule mechanisms, and use of MD simulation in combination with other techniques. This review provides comprehensive summaries of the mechanisms of plant biomolecules in the environment revealed by MD simulation and validates it as an applicable tool for bridging gaps between macroscopic and microscopic behavior, providing insights into the wide application of MD simulation in plant biomolecules.
Collapse
Affiliation(s)
- Jieting Wu
- School of Environmental Science, Liaoning University, Shenyang 110036, People's Republic of China.
| | - Tian Gao
- School of Environmental Science, Liaoning University, Shenyang 110036, People's Republic of China
| | - Haijuan Guo
- School of Environmental Science, Liaoning University, Shenyang 110036, People's Republic of China
| | - Lei Zhao
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, People's Republic of China
| | - Sidi Lv
- School of Environmental Science, Liaoning University, Shenyang 110036, People's Republic of China
| | - Jin Lv
- School of Environmental Science, Liaoning University, Shenyang 110036, People's Republic of China
| | - Ruyi Yao
- School of Environmental Science, Liaoning University, Shenyang 110036, People's Republic of China
| | - Yanyi Yu
- School of Environmental Science, Liaoning University, Shenyang 110036, People's Republic of China
| | - Fang Ma
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, People's Republic of China
| |
Collapse
|
15
|
González-Paz L, Lossada C, Hurtado-León ML, Fernández-Materán FV, Paz JL, Parvizi S, Cardenas Castillo RE, Romero F, Alvarado YJ. Intrinsic Dynamics of the ClpXP Proteolytic Machine Using Elastic Network Models. ACS Omega 2023; 8:7302-7318. [PMID: 36873006 PMCID: PMC9979342 DOI: 10.1021/acsomega.2c04347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 10/25/2022] [Indexed: 06/18/2023]
Abstract
ClpXP complex is an ATP-dependent mitochondrial matrix protease that binds, unfolds, translocates, and subsequently degrades specific protein substrates. Its mechanisms of operation are still being debated, and several have been proposed, including the sequential translocation of two residues (SC/2R), six residues (SC/6R), and even long-pass probabilistic models. Therefore, it has been suggested to employ biophysical-computational approaches that can determine the kinetics and thermodynamics of the translocation. In this sense, and based on the apparent inconsistency between structural and functional studies, we propose to apply biophysical approaches based on elastic network models (ENM) to study the intrinsic dynamics of the theoretically most probable hydrolysis mechanism. The proposed models ENM suggest that the ClpP region is decisive for the stabilization of the ClpXP complex, contributing to the flexibility of the residues adjacent to the pore, favoring the increase in pore size and, therefore, with the energy of interaction of its residues with a larger portion of the substrate. It is predicted that the complex may undergo a stable configurational change once assembled and that the deformability of the system once assembled is oriented, to increase the rigidity of the domains of each region (ClpP and ClpX) and to gain flexibility of the pore. Our predictions could suggest under the conditions of this study the mechanism of the interaction of the system, of which the substrate passes through the unfolding of the pore in parallel with a folding of the bottleneck. The variations in the distance calculated by molecular dynamics could allow the passage of a substrate with a size equivalent to ∼3 residues. The theoretical behavior of the pore and the stability and energy of binding to the substrate based on ENM models suggest that in this system, there are thermodynamic, structural, and configurational conditions that allow a possible translocation mechanism that is not strictly sequential.
Collapse
Affiliation(s)
- Lenin González-Paz
- Facultad
Experimental de Ciencias (FEC), Departamento de Biología, Laboratorio
de Genética y Biología Molecular (LGBM), Universidad del Zulia (LUZ), 4001 Maracaibo, Zulia, República Bolivariana
de Venezuela
- Centro
de Biomedicina Molecular (CBM). Laboratorio de Biocomputación
(LB), Instituto Venezolano de Investigaciones
Científicas (IVIC), 4001 Maracaibo, Zulia, República Bolivariana de Venezuela
| | - Carla Lossada
- Centro
de Biomedicina Molecular (CBM). Laboratorio de Biocomputación
(LB), Instituto Venezolano de Investigaciones
Científicas (IVIC), 4001 Maracaibo, Zulia, República Bolivariana de Venezuela
| | - Maria Laura Hurtado-León
- Facultad
Experimental de Ciencias (FEC), Departamento de Biología, Laboratorio
de Genética y Biología Molecular (LGBM), Universidad del Zulia (LUZ), 4001 Maracaibo, Zulia, República Bolivariana
de Venezuela
| | - Francelys V. Fernández-Materán
- Centro
de Biomedicina Molecular (CBM). Laboratorio de Biocomputación
(LB), Instituto Venezolano de Investigaciones
Científicas (IVIC), 4001 Maracaibo, Zulia, República Bolivariana de Venezuela
| | - José Luis Paz
- Departamento
Académico de Química Inorgánica, Facultad de
Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos, 15081 Lima, Perú
| | - Shayan Parvizi
- Pulmonary,
Critical Care and Sleep Medicine, Baylor
College of Medicine, Houston, Texas 77030, United States
| | | | - Freddy Romero
- Pulmonary,
Critical Care and Sleep Medicine, Baylor
College of Medicine, Houston, Texas 77030, United States
| | - Ysaias J. Alvarado
- Centro
de Biomedicina Molecular (CBM), Laboratorio de Química Biofísica
Teórica y Experimental (LQBTE), Instituto
Venezolano de Investigaciones Cientificas (IVIC), 4001 Maracaibo, Zulia, República Bolivariana de Venezuela
| |
Collapse
|
16
|
Nema S, Verma K, Mani A, Maurya NS, Tiwari A, Bharti PK. Identification of Potential Antimalarial Drug Candidates Targeting Falcipain-2 Protein of Malaria Parasite-A Computational Strategy. BioTech (Basel) 2022; 11:biotech11040054. [PMID: 36546908 PMCID: PMC9775493 DOI: 10.3390/biotech11040054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 11/28/2022] [Accepted: 11/28/2022] [Indexed: 12/02/2022]
Abstract
Falcipain-2 (FP-2) is one of the main haemoglobinase of P. falciparum which is an important molecular target for the treatment of malaria. In this study, we have screened alkaloids to identify potential inhibitors against FP-2 since alkaloids possess great potential as anti-malarial agents. A total of 340 alkaloids were considered for the study using a series of computational pipelines. Initially, pharmacokinetics and toxicity risk assessment parameters were applied to screen compounds. Subsequently, molecular docking algorithms were utilised to understand the binding efficiency of alkaloids against FP-2. Further, oral toxicity prediction was done using the pkCSM tool, and 3D pharmacophore features were analysed using the PharmaGist server. Finally, MD simulation was performed for Artemisinin and the top 3 drug candidates (Noscapine, Reticuline, Aclidinium) based on docking scores to understand the functional impact of the complexes, followed by a binding site interaction residues study. Overall analysis suggests that Noscapine conceded good pharmacokinetics and oral bioavailability properties. Also, it showed better binding efficiency with FP-2 when compared to Artemisinin. Interestingly, structure alignment analysis with artemisinin revealed that Noscapine, Reticuline, and Aclidinium might possess similar biological action. Molecular dynamics and free energy calculations revealed that Noscapine could be a potent antimalarial agent targeting FP-2 that can be used for the treatment of malaria and need to be studied experimentally in the future.
Collapse
Affiliation(s)
- Shrikant Nema
- Division of Vector-Borne Diseases, ICMR-National Institute of Research in Tribal Health, Jabalpur 482 003, Madhya Pradesh, India
- School of Biotechnology, Rajiv Gandhi Proudyogiki Vishwavidyalaya (State Technological University of Madhya Pradesh), Bhopal 462 023, Madhya Pradesh, India
| | - Kanika Verma
- Division of Vector-Borne Diseases, ICMR-National Institute of Research in Tribal Health, Jabalpur 482 003, Madhya Pradesh, India
| | - Ashutosh Mani
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad 211 004, Uttar Pradesh, India
| | - Neha Shree Maurya
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad 211 004, Uttar Pradesh, India
| | - Archana Tiwari
- School of Biotechnology, Rajiv Gandhi Proudyogiki Vishwavidyalaya (State Technological University of Madhya Pradesh), Bhopal 462 023, Madhya Pradesh, India
| | - Praveen Kumar Bharti
- Division of Vector-Borne Diseases, ICMR-National Institute of Research in Tribal Health, Jabalpur 482 003, Madhya Pradesh, India
- Correspondence:
| |
Collapse
|
17
|
Samanta S, Banerjee J, Das B, Mandal J, Chatterjee S, Ali KM, Sinha S, Giri B, Ghosh T, Dash SK. Antibacterial potency of cytocompatible chitosan-decorated biogenic silver nanoparticles and molecular insights towards cell-particle interaction. Int J Biol Macromol 2022; 219:919-939. [PMID: 35961557 DOI: 10.1016/j.ijbiomac.2022.08.050] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 07/23/2022] [Accepted: 08/07/2022] [Indexed: 02/06/2023]
Abstract
In the study, leaf extract of Carica papaya was utilized for the biogenic fabrication process of chitosan functionalized silver nanoparticles (Ag-Chito NPs). HRTEM analysis revealed that the fabricated Ag-Chito NPs was spherical in shape, with an average particle size of 13.31 (±0.07) nm. FTIR, UV-Vis, DLS, and other characterizations were also performed to analyze the diverse physicochemical properties of the particles. The antibacterial potency of the synthesized Ag-Chito NPs was tested against the two clinically isolated multidrug resistant uropathogenic bacterial strains, i.e. MLD 2 (Escherichia coli) and MLD 4 (Staphylococcus aureus) through MIC, MBC, time and concentration dependent killing kinetic assay, inhibition of biofilm formation assay, fluorescence and SEM imaging. Significantly, Ag-Chito NPs showed the highest sensitivity against the MLD 2 (MIC value of 12.5 μg/mL) strain, as compared to the MLD 4 (MIC value of 15 μg/mL) strain. From the hemolysis assay, it was revealed that Ag-Chito NPs exerted no significant toxicity up to 50 μg/mL against healthy human blood cells. Additionally, in silico analysis of chitosan (functionalized on the surface of AgNPs) and bacterial cell membrane protein also evidently suggested a strong interaction between Ag-Chito NPs and bacterial cells, which might be responsible for bacterial cell death.
Collapse
Affiliation(s)
- Sovan Samanta
- Department of Physiology, University of Gour Banga, Malda 732103, West Bengal, India
| | - Jhimli Banerjee
- Department of Physiology, University of Gour Banga, Malda 732103, West Bengal, India
| | - Balaram Das
- Department of Physiology, Belda College, Paschim Medinipur 721424, West Bengal, India
| | - Jayanta Mandal
- Department of Botany, Vivekananda Mahavidyalaya, Haripal, Hooghly 712405, West Bengal, India
| | | | - Kazi Monjur Ali
- Department of Nutrition, M.U.C Women's College, Purba Bardhaman 713104, West Bengal, India
| | - Sangram Sinha
- Department of Botany, Vivekananda Mahavidyalaya, Haripal, Hooghly 712405, West Bengal, India
| | - Biplab Giri
- Department of Physiology, University of Gour Banga, Malda 732103, West Bengal, India
| | - Totan Ghosh
- Department of Applied Chemistry, Maulana Abul Kalam Azad University of Technology, 741249, West Bengal, India
| | - Sandeep Kumar Dash
- Department of Physiology, University of Gour Banga, Malda 732103, West Bengal, India.
| |
Collapse
|
18
|
Xiong Y, Gao X, Pan D, Zhang T, Qi L, Wang N, Zhao Y, Dang Y. A strategy for screening novel umami dipeptides based on common feature pharmacophore and molecular docking. Biomaterials 2022; 288:121697. [DOI: 10.1016/j.biomaterials.2022.121697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 07/21/2022] [Indexed: 11/16/2022]
|
19
|
Gao K, Wang R, Chen J, Cheng L, Frishcosy J, Huzumi Y, Qiu Y, Schluckbier T, Wei X, Wei GW. Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2. Chem Rev 2022; 122:11287-11368. [PMID: 35594413 PMCID: PMC9159519 DOI: 10.1021/acs.chemrev.1c00965] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Despite tremendous efforts in the past two years, our understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), virus-host interactions, immune response, virulence, transmission, and evolution is still very limited. This limitation calls for further in-depth investigation. Computational studies have become an indispensable component in combating coronavirus disease 2019 (COVID-19) due to their low cost, their efficiency, and the fact that they are free from safety and ethical constraints. Additionally, the mechanism that governs the global evolution and transmission of SARS-CoV-2 cannot be revealed from individual experiments and was discovered by integrating genotyping of massive viral sequences, biophysical modeling of protein-protein interactions, deep mutational data, deep learning, and advanced mathematics. There exists a tsunami of literature on the molecular modeling, simulations, and predictions of SARS-CoV-2 and related developments of drugs, vaccines, antibodies, and diagnostics. To provide readers with a quick update about this literature, we present a comprehensive and systematic methodology-centered review. Aspects such as molecular biophysics, bioinformatics, cheminformatics, machine learning, and mathematics are discussed. This review will be beneficial to researchers who are looking for ways to contribute to SARS-CoV-2 studies and those who are interested in the status of the field.
Collapse
Affiliation(s)
- Kaifu Gao
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Rui Wang
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Jiahui Chen
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Limei Cheng
- Clinical
Pharmacology and Pharmacometrics, Bristol
Myers Squibb, Princeton, New Jersey 08536, United States
| | - Jaclyn Frishcosy
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuta Huzumi
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuchi Qiu
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Tom Schluckbier
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Xiaoqi Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Guo-Wei Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Electrical and Computer Engineering, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
| |
Collapse
|
20
|
Wylie MR, Merrell DS. The Antimicrobial Potential of the Neem Tree Azadirachta indica. Front Pharmacol 2022; 13:891535. [PMID: 35712721 PMCID: PMC9195866 DOI: 10.3389/fphar.2022.891535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/09/2022] [Indexed: 12/24/2022] Open
Abstract
Azadirachta indica (A. Juss), also known as the neem tree, has been used for millennia as a traditional remedy for a multitude of human ailments. Also recognized around the world as a broad-spectrum pesticide and fertilizer, neem has applications in agriculture and beyond. Currently, the extensive antimicrobial activities of A. indica are being explored through research in the fields of dentistry, food safety, bacteriology, mycology, virology, and parasitology. Herein, some of the most recent studies that demonstrate the potential of neem as a previously untapped source of novel therapeutics are summarized as they relate to the aforementioned research topics. Additionally, the capacity of neem extracts and compounds to act against drug-resistant and biofilm-forming organisms, both of which represent large groups of pathogens for which there are limited treatment options, are highlighted. Updated information on the phytochemistry and safety of neem-derived products are discussed as well. Although there is a growing body of exciting evidence that supports the use of A. indica as an antimicrobial, additional studies are clearly needed to determine the specific mechanisms of action, clinical efficacy, and in vivo safety of neem as a treatment for human pathogens of interest. Moreover, the various ongoing studies and the diverse properties of neem discussed herein may serve as a guide for the discovery of new antimicrobials that may exist in other herbal panaceas across the globe.
Collapse
Affiliation(s)
- Marina R Wylie
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - D Scott Merrell
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| |
Collapse
|
21
|
Bhar A, Jain A, Das S. Natural therapeutics against SARS CoV2: the potentiality and challenges. Vegetos 2022; 36:322-331. [PMID: 35729947 PMCID: PMC9198211 DOI: 10.1007/s42535-022-00401-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 04/24/2022] [Accepted: 04/29/2022] [Indexed: 11/28/2022]
Abstract
The incidence of the COVID-19 pandemic completely reoriented global socio-economic parameters and human civilization have experienced the worst situation in the recent past. The rapid mutation rates in viruses have continuously been creating emerging variants of concerns (VOCs) which devastated different parts of the world with subsequent waves of infection. Although, series of antiviral drugs and vaccines were formulated but cent percent effectiveness of these drugs is still awaited. Many of these drugs have different side effects which necessitate proper trial before release. Plants are the storehouse of antimicrobial metabolites which have also long been utilized as traditional medicines against different viral infections. Although, proper mechanism of action of these traditional medicines are unknown, they may be a potential source of effective anti-COVID drug for future implications. Advanced bioinformatic applications have opened up a new arena in predicting these repurposed drugs as a potential COVID mitigator. The present review summarizes brief accounts of the corona virus with their possible entry mechanism. This study also tries to classify different possible anti COVID-19 plant-derived metabolites based on their probable mode of action. This review will surely provide useful information on repurposed drugs to combat COVID-19 in this critical situation.
Collapse
Affiliation(s)
- Anirban Bhar
- Post Graduate Department of Botany, Ramakrishna Mission Vivekananda Centenary College, Rahara, Kolkata, 700118 India
| | - Akansha Jain
- Division of Plant Biology, Bose Institute, Centenary Campus, P 1/12, CIT Scheme, VII-M, Kolkata, West Bengal 700054 India
| | - Sampa Das
- Division of Plant Biology, Bose Institute, Centenary Campus, P 1/12, CIT Scheme, VII-M, Kolkata, West Bengal 700054 India
| |
Collapse
|
22
|
Xiao X, Peng Y, Wang Z, Zhang L, Yang T, Sun Y, Chen Y, Zhang W, Chang X, Huang W, Tian S, Feng Z, Xinhua N, Tang Q, Mao Y. A novel immune checkpoint siglec-15 antibody inhibits LUAD by modulating mφ polarization in TME. Pharmacol Res 2022; 181:106269. [PMID: 35605813 DOI: 10.1016/j.phrs.2022.106269] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 05/10/2022] [Accepted: 05/18/2022] [Indexed: 12/22/2022]
Abstract
BACKGROUND Siglec-15 (S15) is a type-I transmembrane protein and is considered a new candidate of immune checkpoint inhibitor for cancer immunotherapy. METHODS In the present study, we first constructed and characterized a chimeric S15-specific monoclonal antibody (S15-4E6A). Then, the antitumor effectiveness and modulatory role of S15-4E6A in macrophages (mφs) were explored in vitro and in vivo. Finally, the underlying mechanism by which S15mAb inhibits LUAD was preliminarily explored. RESULTS The results demonstrated the successful construction of S15-4E6A, and S15-4E6A exerted an efficacious tumor-inhibitory effect on LUAD cells and xenografts. S15-4E6A could promote M1-mφ polarization while inhibiting M2-mφ polarization, both in vitro and in vivo. CONCLUSIONS S15-based immunotherapy that functions by modulating mφ polarization may be a promising strategy for the treatment of S15-positive LUAD.
Collapse
Affiliation(s)
- Xuejun Xiao
- Department of Pharmacology, Xinjiang Medical University, Urumqi, China
| | - Yan Peng
- NHC Key Laboratory of Antibody Technique, Nanjing Medical University, Nanjing, China; Jiangsu Province Engineering Research Center of Antibody Drug, Nanjing Medical University, Nanjing, China; Department of Pathology, Nanjing Medical University, Nanjing, China
| | - Zheyue Wang
- NHC Key Laboratory of Antibody Technique, Nanjing Medical University, Nanjing, China; Jiangsu Province Engineering Research Center of Antibody Drug, Nanjing Medical University, Nanjing, China; Department of Pathology, Nanjing Medical University, Nanjing, China
| | - Louqian Zhang
- Department of Thoracic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Tingting Yang
- NHC Key Laboratory of Antibody Technique, Nanjing Medical University, Nanjing, China; Jiangsu Province Engineering Research Center of Antibody Drug, Nanjing Medical University, Nanjing, China; Department of Pathology, Nanjing Medical University, Nanjing, China
| | - Yangyang Sun
- Department of Pathology, Changzhou No. 2 People's Hospital Affiliated with Nanjing Medical University, Changzhou, China
| | - Yufeng Chen
- NHC Key Laboratory of Antibody Technique, Nanjing Medical University, Nanjing, China; Jiangsu Province Engineering Research Center of Antibody Drug, Nanjing Medical University, Nanjing, China; Department of Pathology, Nanjing Medical University, Nanjing, China
| | - Wenqing Zhang
- NHC Key Laboratory of Antibody Technique, Nanjing Medical University, Nanjing, China; Jiangsu Province Engineering Research Center of Antibody Drug, Nanjing Medical University, Nanjing, China; Department of Pathology, Nanjing Medical University, Nanjing, China
| | - Xinxia Chang
- NHC Key Laboratory of Antibody Technique, Nanjing Medical University, Nanjing, China; Jiangsu Province Engineering Research Center of Antibody Drug, Nanjing Medical University, Nanjing, China; Department of Pathology, Nanjing Medical University, Nanjing, China
| | - Wen Huang
- Department of Oncology, The Fourth Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Shuning Tian
- NHC Key Laboratory of Antibody Technique, Nanjing Medical University, Nanjing, China; Jiangsu Province Engineering Research Center of Antibody Drug, Nanjing Medical University, Nanjing, China
| | - Zhenqing Feng
- NHC Key Laboratory of Antibody Technique, Nanjing Medical University, Nanjing, China; Jiangsu Province Engineering Research Center of Antibody Drug, Nanjing Medical University, Nanjing, China; Department of Pathology, Nanjing Medical University, Nanjing, China
| | - Nabi Xinhua
- Department of Pharmacology, Xinjiang Medical University, Urumqi, China.
| | - Qi Tang
- NHC Key Laboratory of Antibody Technique, Nanjing Medical University, Nanjing, China; Jiangsu Province Engineering Research Center of Antibody Drug, Nanjing Medical University, Nanjing, China; Department of Pathology, Changzhou No. 2 People's Hospital Affiliated with Nanjing Medical University, Changzhou, China.
| | - Yuan Mao
- Department of Oncology, The Fourth Affiliated Hospital of Nanjing Medical University, Nanjing, China; Department of Oncology, Geriatric Hospital of Nanjing Medical University, Nanjing, China; Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, China.
| |
Collapse
|
23
|
Raafat A, Mowafy S, Abouseri SM, Fouad MA, Farag NA. Lead generation of cysteine based mesenchymal epithelial transition (c-Met) kinase inhibitors: Using structure-based scaffold hopping, 3D-QSAR pharmacophore modeling, virtual screening, molecular docking, and molecular dynamics simulation. Comput Biol Med 2022; 146:105526. [PMID: 35487125 DOI: 10.1016/j.compbiomed.2022.105526] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 03/22/2022] [Accepted: 04/07/2022] [Indexed: 11/24/2022]
Abstract
Cysteine-based mesenchymal-epithelial transition (c-Met) is a receptor tyrosine kinase that plays a definitive role during cancer progression and was identified as a possible target for anti-angiogenesis drugs. In the present study, different protocols of computer-based drug design were performed. Construction of predictive pharmacophore model using HypoGen algorithm resulted in a validated model of four features of positive ionizable, hydrogen bond acceptor, hydrophobic, and ring aromatic features with a correlation coefficient of 0.87, a configuration cost of 14.95, and a cost difference of 357.92. The model revealed a promising predictive power and had >90% probability of representing true correlation with the activity data. The model was established using Fisher's validation test at the 95% confidence level and test set prediction (r = 0.96), furthermore, the model was validated by mapping of set of compounds undergoing clinical trials as class Ⅱ c-met inhibitors. The generated valid pharmacophore model was then anticipated for virtual screening of three data bases. Moreover, scaffold hopping using replace fragments protocol was implemented. Hits generated were filtered according to Lipinski's rule; 510 selected hits were anatomized and subjected to molecular docking studies into the crystal structure of c-Met kinase. The good correlation between docking scores and ligand pharmacophore mapping fit values provided a reliable foundation for designing new potentially active candidates that may target c-Met kinase. Eventually, eight hits were selected as potential leads. Subsequently, seven (Hits) have displayed a higher dock score and demonstrated key residue interactions with stable molecular dynamics simulation. Therefore, these c-Met kinase inhibitors may further serve as new chemical spaces in designing new compounds.
Collapse
|
24
|
Rudrapal M, Celik I, Khan J, Ansari MA, Alomary MN, Yadav R, Sharma T, Tallei TE, Pasala PK, Sahoo RK, Khairnar SJ, Bendale AR, Zothantluanga JH, Chetia D, Walode SG. Identification of bioactive molecules from Triphala (Ayurvedic herbal formulation) as potential inhibitors of SARS-CoV-2 main protease (Mpro) through computational investigations. J King Saud Univ Sci 2022; 34:101826. [PMID: 35035181 PMCID: PMC8744360 DOI: 10.1016/j.jksus.2022.101826] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 12/20/2021] [Accepted: 01/05/2022] [Indexed: 05/28/2023]
Abstract
Severe acute respiratory syndrome coronavirus disease (SARS-CoV-2) induced coronavirus disease 2019 (COVID-19) pandemic is the present worldwide health emergency. The global scientific community faces a significant challenge in developing targeted therapies to combat the SARS-CoV-2 infection. Computational approaches have been critical for identifying potential SARS-CoV-2 inhibitors in the face of limited resources and in this time of crisis. Main protease (Mpro) is an intriguing drug target because it processes the polyproteins required for SARS-CoV-2 replication. The application of Ayurvedic knowledge from traditional Indian systems of medicine may be a promising strategy to develop potential inhibitor for different target proteins of SARS-CoV-2. With this endeavor, we docked bioactive molecules from Triphala, an Ayurvedic formulation, against Mpro followed by molecular dynamics (MD) simulation (100 ns) to investigate their inhibitory potential against SARS-CoV-2. The top four best docked molecules (terflavin A, chebulagic acid, chebulinic acid, and corilagin) were selected for MD simulation study and the results obtained were compared to native ligand X77. From docking and MD simulation studies, the selected molecules showed promising binding affinity with the formation of stable complexes at the active binding pocket of Mpro and exhibited negative binding energy during MM-PBSA calculations, indication their strong binding affinity with the target protein. The identified bioactive molecules were further analyzed for drug-likeness by Lipinski's filter, ADMET and toxicity studies. Computational (in silico) investigations identified terflavin A, chebulagic acid, chebulinic acid, and corilagin from Triphala formulation as promising inhibitors of SARS-CoV-2 Mpro, suggesting experimental (in vitro/in vivo) studies to further explore their inhibitory mechanisms.
Collapse
Affiliation(s)
- Mithun Rudrapal
- Department of Pharmaceutical Chemistry, Rasiklal M. Dhariwal Institute of Pharmaceutical Education & Research, Pune 411019, Maharashtra, India
| | - Ismail Celik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University, Kayseri 38039, Turkey
| | - Johra Khan
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah 11952, Saudi Arabia
- Health and Basic Sciences Research Center, Majmaah University, Al Majmaah 11952, Saudi Arabia
| | - Mohammad Azam Ansari
- Department of Epidemic Disease Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabaia
| | - Mohammad N Alomary
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah 11952, Saudi Arabia
- Health and Basic Sciences Research Center, Majmaah University, Al Majmaah 11952, Saudi Arabia
- National Centre for Biotechnology, King Abdulaziz City for Science and Technology (KACST), Riyadh 11442, Saudi Arabia
| | - Rohitash Yadav
- Department of Pharmacology, All India Institute of Medical Sciences, Rishikesh 249203, India
| | - Tripti Sharma
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Siksha O Anusandhan Deemed to be University, Bhubaneswar 751003, Odisha, India
| | - Trina Ekawati Tallei
- Department of Biology, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, North Sulawesi, Indonesia
- The University Center of Excellence for Biotechnology and Conservation of Wallacea, Sam Ratulangi University, Manado, North Sulawesi 95115, Indonesia
| | | | - Ranjan Kumar Sahoo
- School of Pharmacy and Life Sciences, Centurion University of Technology and Management, Bhubaneswar 752050, Odisha, India
| | | | - Atul R Bendale
- Sandip Institute of Pharmaceutical Sciences, Nashik 422213, India
| | - James H Zothantluanga
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh 786004, Assam, India
| | - Dipak Chetia
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh 786004, Assam, India
| | - Sanjay G Walode
- Department of Pharmaceutical Chemistry, Rasiklal M. Dhariwal Institute of Pharmaceutical Education & Research, Pune 411019, Maharashtra, India
| |
Collapse
|
25
|
Haddad M, Gaudreault R, Sasseville G, Nguyen PT, Wiebe H, Van De Ven T, Bourgault S, Mousseau N, Ramassamy C. Molecular Interactions of Tannic Acid with Proteins Associated with SARS-CoV-2 Infectivity. Int J Mol Sci 2022; 23:2643. [PMID: 35269785 PMCID: PMC8910432 DOI: 10.3390/ijms23052643] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/16/2022] [Accepted: 02/23/2022] [Indexed: 02/01/2023] Open
Abstract
The overall impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on our society is unprecedented. The identification of small natural ligands that could prevent the entry and/or replication of the coronavirus remains a pertinent approach to fight the coronavirus disease (COVID-19) pandemic. Previously, we showed that the phenolic compounds corilagin and 1,3,6-tri-O-galloyl-β-D-glucose (TGG) inhibit the interaction between the SARS-CoV-2 spike protein receptor binding domain (RBD) and angiotensin-converting enzyme 2 (ACE2), the SARS-CoV-2 target receptor on the cell membrane of the host organism. Building on these promising results, we now assess the effects of these phenolic ligands on two other crucial targets involved in SARS-CoV-2 cell entry and replication, respectively: transmembrane protease serine 2 (TMPRSS2) and 3-chymotrypsin like protease (3CLpro) inhibitors. Since corilagin, TGG, and tannic acid (TA) share many physicochemical and structural properties, we investigate the binding of TA to these targets. In this work, a combination of experimental methods (biochemical inhibition assays, surface plasmon resonance, and quartz crystal microbalance with dissipation monitoring) confirms the potential role of TA in the prevention of SARS-CoV-2 infectivity through the inhibition of extracellular RBD/ACE2 interactions and TMPRSS2 and 3CLpro activity. Moreover, molecular docking prediction followed by dynamic simulation and molecular mechanics Poisson–Boltzmann surface area (MMPBSA) free energy calculation also shows that TA binds to RBD, TMPRSS2, and 3CLpro with higher affinities than TGG and corilagin. Overall, these results suggest that naturally occurring TA is a promising candidate to prevent and inhibit the infectivity of SARS-CoV-2.
Collapse
|
26
|
Li M, Liu X, Zhang S, Liang S, Zhang Q, Chen J. Deciphering binding mechanism of inhibitors to SARS-COV-2 main protease through multiple replica accelerated molecular dynamics simulations and free energy landscapes. Phys Chem Chem Phys 2022; 24:22129-22143. [DOI: 10.1039/d2cp03446h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The pneumonia outbreak caused by the SARS-CoV-2 virus poses a serious threat to human health and the world economy. Development of safe and highly effective antiviral drugs is of great...
Collapse
|
27
|
Üstün E, Düşünceli SD, Coşkun F, Özdemir İ. Molybdenum Carbonyl Complexes with Benzimidazole Derivatives Against SARS-CoV-2 by Molecular Docking and DFT/TDDFT Methods. J Comput Biophys Chem 2021. [DOI: 10.1142/s2737416521500502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Benzimidazole derivative molecules attract attention of scientists due to their bioactivities. The dramatic changes in recorded activities according to the type and position of the substituents motivate synthesis and analysis of new molecules. Commercial benzimidazole-based molecules have been used in therapeutic procedures. It is known that the activities of metal complexes with benzimidazole derivative ligands have different activities when compared to the benzimidazole main structure. Nowadays, one of the most important health problems is COVID-19, which caused the pandemic that we are still experiencing. Although vaccine studies are important to overcome acute problems, regarding the possible post-vaccination adverse effects, the need for new drugs against the virus is obvious. Considering the urgency and the limited facilities during the pandemic, preliminary in silico studies of candidate molecules are essential. In this study, {[bis-(N-benzylbenzimidazole)] tetracarbonylmolybdenum}, {[bis-(N-4-chlorobenzylbenzimidazole)] tetracarbonylmolybdenum} and {[bis-(N-4-methoxybenzylbenzimidazole)] tetracarbonylmolybdenum} were synthesized and characterized. The optimization and the structural analysis of these molecules were performed by DFT/TDDFT methods. The molecules were docked into SARS coronavirus main peptidase (PDB ID: 2gtb), COVID-19 main protease in complex with Z219104216 (PDB ID: 5r82), COVID-19 main protease in complex with an inhibitor N3 (PDB ID: 6lu7) and Papain-like protease of SARS-CoV-2 (PDB ID: 6w9c) crystal structures for evaluation of their anti-viral activity.
Collapse
Affiliation(s)
- Elvan Üstün
- Department of Chemistry, Faculty of Art and Science, Ordu University, 52200 Ordu, Turkey
| | - Serpil Demir Düşünceli
- Department of Chemistry Faculty of Art and Science, İnönü University, 44280 Malatya, Turkey
- Catalysis Research and Application Center, İnönü University, 44280 Malatya, Turkey
| | - Feyzullah Coşkun
- Department of Chemistry Faculty of Art and Science, İnönü University, 44280 Malatya, Turkey
- Catalysis Research and Application Center, İnönü University, 44280 Malatya, Turkey
| | - İsmail Özdemir
- Department of Chemistry Faculty of Art and Science, İnönü University, 44280 Malatya, Turkey
- Catalysis Research and Application Center, İnönü University, 44280 Malatya, Turkey
| |
Collapse
|
28
|
Montone CM, Aita SE, Arnoldi A, Capriotti AL, Cavaliere C, Cerrato A, Lammi C, Piovesana S, Ranaldi G, Laganà A. Characterization of the Trans-Epithelial Transport of Green Tea ( C. sinensis) Catechin Extracts with In Vitro Inhibitory Effect against the SARS-CoV-2 Papain-like Protease Activity. Molecules 2021; 26:molecules26216744. [PMID: 34771162 PMCID: PMC8587865 DOI: 10.3390/molecules26216744] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/15/2021] [Accepted: 11/05/2021] [Indexed: 12/28/2022] Open
Abstract
This work describes an untargeted analytical approach for the screening, identification, and characterization of the trans-epithelial transport of green tea (Camellia sinensis) catechin extracts with in vitro inhibitory effect against the SARS-CoV-2 papain-like protease (PLpro) activity. After specific catechin extraction, a chromatographic separation obtained six fractions were carried out. The fractions were assessed in vitro against the PLpro target. Fraction 5 showed the highest inhibitory activity against the SARS-CoV-2 PLpro (IC50 of 0.125 μg mL-1). The untargeted characterization revealed that (-)-epicatechin-3-gallate (ECG) was the most abundant compound in the fraction and the primary molecule absorbed by differentiated Caco-2 cells. Results indicated that fraction 5 was approximately 10 times more active than ECG (IC50 value equal to 11.62 ± 0.47 μg mL-1) to inhibit the PLpro target. Overall, our findings highlight the synergistic effects of the various components of the crude extract compared to isolated ECG.
Collapse
Affiliation(s)
- Carmela Maria Montone
- Dipartimento di Chimica, Università di Roma La Sapienza, Piazzale Aldo Moro 5, 00185 Roma, Italy; (C.M.M.); (S.E.A.); (C.C.); (A.C.); (S.P.); (A.L.)
| | - Sara Elsa Aita
- Dipartimento di Chimica, Università di Roma La Sapienza, Piazzale Aldo Moro 5, 00185 Roma, Italy; (C.M.M.); (S.E.A.); (C.C.); (A.C.); (S.P.); (A.L.)
| | - Anna Arnoldi
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano La Statale, Via Mangiagalli, 25, 20133 Milano, Italy;
| | - Anna Laura Capriotti
- Dipartimento di Chimica, Università di Roma La Sapienza, Piazzale Aldo Moro 5, 00185 Roma, Italy; (C.M.M.); (S.E.A.); (C.C.); (A.C.); (S.P.); (A.L.)
- Correspondence: (A.L.C.); (C.L.); Tel.: +39-06-4991-3945 (A.L.C.); +39-02503-19372 (C.L.)
| | - Chiara Cavaliere
- Dipartimento di Chimica, Università di Roma La Sapienza, Piazzale Aldo Moro 5, 00185 Roma, Italy; (C.M.M.); (S.E.A.); (C.C.); (A.C.); (S.P.); (A.L.)
| | - Andrea Cerrato
- Dipartimento di Chimica, Università di Roma La Sapienza, Piazzale Aldo Moro 5, 00185 Roma, Italy; (C.M.M.); (S.E.A.); (C.C.); (A.C.); (S.P.); (A.L.)
| | - Carmen Lammi
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano La Statale, Via Mangiagalli, 25, 20133 Milano, Italy;
- Correspondence: (A.L.C.); (C.L.); Tel.: +39-06-4991-3945 (A.L.C.); +39-02503-19372 (C.L.)
| | - Susy Piovesana
- Dipartimento di Chimica, Università di Roma La Sapienza, Piazzale Aldo Moro 5, 00185 Roma, Italy; (C.M.M.); (S.E.A.); (C.C.); (A.C.); (S.P.); (A.L.)
| | - Giulia Ranaldi
- CREA, Food and Nutrition Research Centre, 00100 Rome, Italy;
| | - Aldo Laganà
- Dipartimento di Chimica, Università di Roma La Sapienza, Piazzale Aldo Moro 5, 00185 Roma, Italy; (C.M.M.); (S.E.A.); (C.C.); (A.C.); (S.P.); (A.L.)
- CNR NANOTEC, Campus Ecotekne, University of Salento, Via Monteroni, 73100 Lecce, Italy
| |
Collapse
|