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Rai P, Garain T, Gupta D. Phytochemical analysis of Tinospora cordifolia and Withania somnifera and their therapeutic activities with special reference to COVID-19. World J Exp Med 2024; 14:95512. [DOI: 10.5493/wjem.v14.i3.95512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 07/19/2024] [Accepted: 07/29/2024] [Indexed: 08/29/2024] Open
Abstract
Various important medicines make use of secondary metabolites that are produced by plants. Medicinal plants, such as Withania somnifera and Tinospora cordifolia, are rich sources of chemically active compounds and are reported to have numerous therapeutic applications. The therapeutic use of medicinal plants is widely mentioned in Ayurveda and has folkloric importance in different parts of the world. The aim of this review is to summarize the phytochemical profiles, folkloric importance, and primary pharmacological activity of W. somnifera and T. cordifolia with emphasis on their action against the novel coronavirus.
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Affiliation(s)
- Prateek Rai
- Chemistry, Amity Institute of Applied Sciences, Amity University, Noida 201301, Uttar Pradesh, India
| | - Tanya Garain
- Chemistry, Amity Institute of Applied Sciences, Amity University, Noida 201301, Uttar Pradesh, India
| | - Deepshikha Gupta
- Chemistry, Amity Institute of Applied Sciences, Amity University, Noida 201301, Uttar Pradesh, India
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Yamin R, Ahmad I, Khalid H, Perveen A, Abbasi SW, Nishan U, Sheheryar S, Moura AA, Ahmed S, Ullah R, Ali EA, Shah M, Chandra Ojha S. Identifying plant-derived antiviral alkaloids as dual inhibitors of SARS-CoV-2 main protease and spike glycoprotein through computational screening. Front Pharmacol 2024; 15:1369659. [PMID: 39086396 PMCID: PMC11288853 DOI: 10.3389/fphar.2024.1369659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 06/04/2024] [Indexed: 08/02/2024] Open
Abstract
COVID-19 is currently considered the ninth-deadliest pandemic, spreading through direct or indirect contact with infected individuals. It has imposed a consistent strain on both the financial and healthcare resources of many countries. To address this challenge, there is a pressing need for the development of new potential therapeutic agents for the treatment of this disease. To identify potential antiviral agents as novel dual inhibitors of SARS-CoV-2, we retrieved 404 alkaloids from 12 selected medicinal antiviral plants and virtually screened them against the renowned catalytic sites and favorable interacting residues of two essential proteins of SARS-CoV-2, namely, the main protease and spike glycoprotein. Based on docking scores, 12 metabolites with dual inhibitory potential were subjected to drug-likeness, bioactivity scores, and drug-like ability analyses. These analyses included the ligand-receptor stability and interactions at the potential active sites of target proteins, which were analyzed and confirmed through molecular dynamic simulations of the three lead metabolites. We also conducted a detailed binding free energy analysis of pivotal SARS-CoV-2 protein inhibitors using molecular mechanics techniques to reveal their interaction dynamics and stability. Overall, our results demonstrated that 12 alkaloids, namely, adouetine Y, evodiamide C, ergosine, hayatinine, (+)-homoaromoline, isatithioetherin C, N,alpha-L-rhamnopyranosyl vincosamide, pelosine, reserpine, toddalidimerine, toddayanis, and zanthocadinanine, are shortlisted as metabolites based on their interactions with target proteins. All 12 lead metabolites exhibited a higher unbound fraction and therefore greater distribution compared with the standards. Particularly, adouetine Y demonstrated high docking scores but exhibited a nonspontaneous binding profile. In contrast, ergosine and evodiamide C showed favorable binding interactions and superior stability in molecular dynamics simulations. Ergosine demonstrated exceptional performance in several key pharmaceutical metrics. Pharmacokinetic evaluations revealed that ergosine exhibited pronounced bioactivity, good absorption, and optimal bioavailability. Additionally, it was predicted not to cause skin sensitivity and was found to be non-hepatotoxic. Importantly, ergosine and evodiamide C emerged as superior drug candidates for dual inhibition of SARS-CoV-2 due to their strong binding affinity and drug-like ability, comparable to known inhibitors like N3 and molnupiravir. This study is limited by its in silico nature and demands the need for future in vitro and in vivo studies to confirm these findings.
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Affiliation(s)
- Ramsha Yamin
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Iqra Ahmad
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Hira Khalid
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Asia Perveen
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Sumra Wajid Abbasi
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Umar Nishan
- Department of Chemistry, Kohat University of Science & Technology, Kohat, Pakistan
| | - Sheheryar Sheheryar
- Department of Animal Science, Federal University of Ceara, Fortaleza, Brazil
| | | | - Sarfraz Ahmed
- Wellman Centre for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Riaz Ullah
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Essam A. Ali
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Mohibullah Shah
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Suvash Chandra Ojha
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
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Bhagavatula D, Hasan TN, Vohra H, Khorami S, Hussain A. Delineating the Antiapoptotic Property of Apigenin as an Antitumor Agent: A Computational and In Vitro Study on HeLa Cells. ACS OMEGA 2024; 9:24751-24760. [PMID: 38882173 PMCID: PMC11170653 DOI: 10.1021/acsomega.4c01300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 05/04/2024] [Accepted: 05/17/2024] [Indexed: 06/18/2024]
Abstract
Apigenin, a flavonoid, is reported to have multiple health benefits including cancer prevention; this study evaluates the drug likeliness and Swiss ADME properties of apigenin. Apoptosis, which is a key hallmark of cancer, is associated with the deregulation of the balance between proapoptotic proteins and antiapoptotic proteins such as BCL-2,BCL-xl, BFL-1, BCL-w, BRAG-16, and MCL-1. The docking studies of apigenin with the mentioned proteins was performed to identify the interactions between the ligand and proteins, which suggested that apigenin was able to bind to most of the proteins similar to the inhibitory molecules of its native structure. A remarkable reduction in the total energy after energy minimization of apigenin-antiapoptotic protein complexes suggested increased stability of the docked complexes. The same complexes were found to be stable over a 10 ns period of molecular simulation at 300 K. These findings advocated the study to evaluate apigenin's potential to inhibit the HeLa cells at 5, 10, and 15 μM concentrations in the clonogenic assay. Apigenin inhibited the colony-forming ability of HeLa cells in a dose-dependent manner over a fortnight. Light microscopy of the treated cells displayed the morphological evidence characteristic of apoptosis in HeLa cells such as blebbing, spike formation, cytoplasmic oozing, and nuclear fragmentation. Thus, these results clearly indicate that apigenin may be used as a potential chemopreventive agent in cervical cancer management.
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Affiliation(s)
- Deepika Bhagavatula
- School of Life Sciences,Manipal Academy of Higher Education, Dubai 345050 ,United Arab Emirates
| | - Tarique Noorul Hasan
- School of Life Sciences,Manipal Academy of Higher Education, Dubai 345050 ,United Arab Emirates
- Department of Molecular Genetics, Sh. Tahnoon Bin Mohammed Medical City (STMC), Al Ain, Pure Health, Abu Dhabi 17822, United Arab Emirates
| | - Huzefa Vohra
- School of Life Sciences,Manipal Academy of Higher Education, Dubai 345050 ,United Arab Emirates
| | - Sherareh Khorami
- School of Life Sciences,Manipal Academy of Higher Education, Dubai 345050 ,United Arab Emirates
| | - Arif Hussain
- School of Life Sciences,Manipal Academy of Higher Education, Dubai 345050 ,United Arab Emirates
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4
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Bhandari RB, Balkrishna A, Maheshkumar K, Arumugam VA. Traditional Formulations for Managing COVID-19: A Systematic Review. JOURNAL OF INTEGRATIVE AND COMPLEMENTARY MEDICINE 2024; 30:420-430. [PMID: 37972056 DOI: 10.1089/jicm.2023.0177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Background: The advancing etiopathogenesis, diagnosis, and treatment of the global coronavirus disease 2019 (COVID-19) pandemic have prompted the medical community to consider Ayurveda, Siddha, and Unani as add-on preventive and therapeutic options. Objective: To explore the effect of standalone or integrative Traditional Formulations (TFs) on selected clinical symptoms and biomarkers of COVID-19. Search strategy: Out of 465 articles identified from PubMed, ScienceDirect, and Scopus, 17 randomized controlled trials (RCTs) with 1646 COVID-19 patients published from January 2020 to February 2022 were included in the study. Inclusion criteria: RCTs that compared the effect of standalone/integrative TFs in decoction, tablet, and powder forms with placebo plus standard care (SC)/placebo/SC as controls involving mild to severe symptomatic COVID-19 patients were included. Data extraction and analysis: Three reviewers independently assessed the titles and abstracts of each article based on the inclusion after deleting duplicates. The relevant full texts were retrieved and examined, and then their data were extracted and double-checked by three independent reviewers using prepared data extraction forms. The primary outcome variables were reverse transcription polymerase chain reaction, fever, cough, dyspnea, myalgia, headache, C-reactive protein (CRP), erythrocyte sedimentation rate (ESR), and D-dimer. Results: The effect of different TFs or integrative TFs was more to inhibit severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) than the controls. There was an increase in fever and cough, a decrease in dyspnea, myalgia, headache, and ESR, no change in CRP, and a slight increase in D-dimer as an effect of TFs. Conclusions: Integrative or standalone TF may be the inexpensive preventive and therapeutic option to inhibit SARS-CoV-2 and its clinical symptoms.
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Affiliation(s)
- Rudra B Bhandari
- Department of Yoga Science, University of Patanjali, Haridwar, India
| | | | - Kuppusamy Maheshkumar
- Department of Physiology, Government Yoga and Naturopathy Medical College and Hospital, Chennai, India
| | - Velan A Arumugam
- University of Patanjali, Haridwar, India
- Department of Yoga, International Institute of Yoga and Naturopathy Medical College, Chengalpattu, Chennai, India
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Kottekad S, Roy S, Dandamudi U. A computational study to probe the binding aspects of potent polyphenolic inhibitors of pancreatic lipase. J Biomol Struct Dyn 2024; 42:3472-3491. [PMID: 37199285 DOI: 10.1080/07391102.2023.2212795] [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: 10/19/2022] [Accepted: 05/07/2023] [Indexed: 05/19/2023]
Abstract
Pancreatic lipase (PL) is a keen target for anti-obesity therapy that reduces dietary fat absorption. Here, we investigated the binding patterns of 220 PL inhibitors having experimental IC50 values, using molecular docking and binding energy calculations. Screening of these compounds illustrated most of them bound at the catalytic site (S1-S2 channel) and a few compounds are at the non-catalytic site (S2-S3 channel/S1-S3 channel) of PL. This binding pattern could be due to structural uniqueness or bias in conformational search. A strong correlation of pIC50 values with SP/XP docking scores, binding energies (ΔGMMGBSA) assured the binding poses are more true positives. Further, understanding of each class and subclasses of polyphenols indicated tannins preferred non-catalytic site wherein binding energies are underestimated due to huge desolvation energy. In contrast, most of the flavonoids and furan-flavonoids have good binding energies due to strong interactions with catalytic residues. While scoring functions limited the understanding of sub-classes of flavonoids. Hence, focused on 55 potent PL inhibitors of IC50 < 5 µM for better in vivo efficacy. The prediction of bioactivity, drug-likeness properties, led to 14 bioactive compounds. The low root mean square deviation (0.1-0.2 nm) of these potent flavonoids and non-flavonoid/non-polyphenols PL-inhibitor complexes during 100 ns molecular dynamics runs (MD) as well as binding energies obtained from both MD and well-tempered metadynamics, support strong binding to catalytic site. Based on the bioactivity, ADMET properties, and binding affinity data of MD and wt-metaD of potent PL-inhibitors suggests Epiafzelechin 3-O-gallate, Sanggenon C, and Sanggenofuran A shall be promising inhibitors at in vivo conditions.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sanjay Kottekad
- Department of Food Safety and Analytical Quality Control Laboratory, Central Food Technological Research Institute, Council of Scientific and Industrial Research, Mysuru, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Sudip Roy
- Prescience Insilico Private Limited, Bangalore, India
| | - Usharani Dandamudi
- Department of Food Safety and Analytical Quality Control Laboratory, Central Food Technological Research Institute, Council of Scientific and Industrial Research, Mysuru, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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Saini R, Kumar V, Patel CN, Sourirajan A, Dev K. Synergistic antibacterial activity of Phyllanthus emblica fruits and its phytocompounds with ampicillin: a computational and experimental study. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024; 397:857-871. [PMID: 37522914 DOI: 10.1007/s00210-023-02624-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 07/11/2023] [Indexed: 08/01/2023]
Abstract
Phyllanthus emblica L. (syn. Emblica officinalis), popularly known as amla, Indian gooseberry, or the King of Rasyana, is a member of Phyllanthaceae family and is traditionally used in Ayurveda as an immunity booster. The present study aimed to investigate the synergistic interaction of Phyllanthus emblica (FPE) fruits and its selected phytocompounds with ampicillin against selected bacteria. Further, an in silico technique was used to find if major phytocompounds of FPE could bind to proteins responsible for antibiotic resistance in bacterial pathogens and enhance the bioactivity of ampicillin. FPE and all the selected phytocompounds were found to have synergistic antibacterial activity with ampicillin against tested bacteria in different combinations. However, ellagic acid and quercetin interactions with ampicillin resulted in maximum bioactivity enhancement of 32-128 folds and 16-277 folds, respectively. In silico analysis revealed strong ellagic acid, quercetin, and rutin binding with penicillin-binding protein (PBP-) 3, further supported by MD simulations. Ellagic acid and quercetin also fulfill Lipinski's rule, showing similar toxicity characteristics to ampicillin. FPE showed synergistic interaction with ampicillin, possibly due to the presence of phytocompounds such as gallic acid, ellagic acid, quercetin, and rutin. Molecular docking and MD simulations showed the strong interaction of ellagic acid and quercetin with PBP-3 protein. Therefore, these compounds can be explored as potential non-toxic drug candidates to combat bacterial antimicrobial resistance.
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Affiliation(s)
- Rakshandha Saini
- Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, PO Sultanpur, Distt. Solan-173229 HP, Bajhol, India
| | - Vikas Kumar
- University Institute of Biotechnology, Chandigarh University, Gharuan, Mohali, Punjab, 140413, India.
| | - Chirag N Patel
- Department of Botany, Bioinformatics and Climate Change Impacts Management, University School of Science, Gujarat University, Ahmedabad, Gujarat, 380009, India
- Biotechnology Research Center, Technology Innovation Institute, Masdar, Abu Dhabi, 9639, United Arab Emirates
| | - Anuradha Sourirajan
- Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, PO Sultanpur, Distt. Solan-173229 HP, Bajhol, India
| | - Kamal Dev
- Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, PO Sultanpur, Distt. Solan-173229 HP, Bajhol, India.
- Department of Pharmacology and Toxicology, Wright State University, Dayton, OH, 45435, USA.
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Shah M, Yamin R, Ahmad I, Wu G, Jahangir Z, Shamim A, Nawaz H, Nishan U, Ullah R, Ali EA, Sheheryar, Chen K. In-silico evaluation of natural alkaloids against the main protease and spike glycoprotein as potential therapeutic agents for SARS-CoV-2. PLoS One 2024; 19:e0294769. [PMID: 38175855 PMCID: PMC10766191 DOI: 10.1371/journal.pone.0294769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 11/08/2023] [Indexed: 01/06/2024] Open
Abstract
Severe Acute Respiratory Syndrome Corona Virus (SARS-CoV-2) is the causative agent of COVID-19 pandemic, which has resulted in global fatalities since late December 2019. Alkaloids play a significant role in drug design for various antiviral diseases, which makes them viable candidates for treating COVID-19. To identify potential antiviral agents, 102 known alkaloids were subjected to docking studies against the two key targets of SARS-CoV-2, namely the spike glycoprotein and main protease. The spike glycoprotein is vital for mediating viral entry into host cells, and main protease plays a crucial role in viral replication; therefore, they serve as compelling targets for therapeutic intervention in combating the disease. From the selection of alkaloids, the top 6 dual inhibitory compounds, namely liensinine, neferine, isoliensinine, fangchinoline, emetine, and acrimarine F, emerged as lead compounds with favorable docked scores. Interestingly, most of them shared the bisbenzylisoquinoline alkaloid framework and belong to Nelumbo nucifera, commonly known as the lotus plant. Docking analysis was conducted by considering the key active site residues of the selected proteins. The stability of the top three ligands with the receptor proteins was further validated through dynamic simulation analysis. The leads underwent ADMET profiling, bioactivity score analysis, and evaluation of drug-likeness and physicochemical properties. Neferine demonstrated a particularly strong affinity for binding, with a docking score of -7.5025 kcal/mol for main protease and -10.0245 kcal/mol for spike glycoprotein, and therefore a strong interaction with both target proteins. Of the lead alkaloids, emetine and fangchinoline demonstrated the lowest toxicity and high LD50 values. These top alkaloids, may support the body's defense and reduce the symptoms by their numerous biological potentials, even though some properties naturally point to their direct antiviral nature. These findings demonstrate the promising anti-COVID-19 properties of the six selected alkaloids, making them potential candidates for drug design. This study will be beneficial in effective drug discovery and design against COVID-19 with negligible side effects.
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Affiliation(s)
- Mohibullah Shah
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Ramsha Yamin
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Iqra Ahmad
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Gang Wu
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Zainab Jahangir
- Department of Computer Science, University of Agriculture Faisalabad, Punjab, Pakistan
| | - Amen Shamim
- Department of Computer Science, University of Agriculture Faisalabad, Punjab, Pakistan
| | - Haq Nawaz
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Umar Nishan
- Department of Chemistry, Kohat University of Science & Technology, Kohat, Pakistan
| | - Riaz Ullah
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Essam A. Ali
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Sheheryar
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza, Brazil
| | - Ke Chen
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
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Saha C, Naskar R, Chakraborty S. Antiviral Flavonoids: A Natural Scaffold with Prospects as Phytomedicines against SARS-CoV2. Mini Rev Med Chem 2024; 24:39-59. [PMID: 37138419 DOI: 10.2174/1389557523666230503105053] [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: 11/25/2022] [Revised: 03/01/2023] [Accepted: 03/13/2023] [Indexed: 05/05/2023]
Abstract
Flavonoids are vital candidates to fight against a wide range of pathogenic microbial infections. Due to their therapeutic potential, many flavonoids from the herbs of traditional medicine systems are now being evaluated as lead compounds to develop potential antimicrobial hits. The emergence of SARS-CoV-2 caused one of the deadliest pandemics that has ever been known to mankind. To date, more than 600 million confirmed cases of SARS-CoV2 infection have been reported worldwide. Situations are worse due to the unavailability of therapeutics to combat the viral disease. Thus, there is an urgent need to develop drugs against SARS-CoV2 and its emerging variants. Here, we have carried out a detailed mechanistic analysis of the antiviral efficacy of flavonoids in terms of their potential targets and structural feature required for exerting their antiviral activity. A catalog of various promising flavonoid compounds has been shown to elicit inhibitory effects against SARS-CoV and MERS-CoV proteases. However, they act in the high-micromolar regime. Thus a proper leadoptimization against the various proteases of SARS-CoV2 can lead to high-affinity SARS-CoV2 protease inhibitors. To enable lead optimization, a quantitative structure-activity relationship (QSAR) analysis has been developed for the flavonoids that have shown antiviral activity against viral proteases of SARS-CoV and MERS-CoV. High sequence similarities between coronavirus proteases enable the applicability of the developed QSAR to SARS-CoV2 proteases inhibitor screening. The detailed mechanistic analysis of the antiviral flavonoids and the developed QSAR models is a step forward toward the development of flavonoid-based therapeutics or supplements to fight against COVID-19.
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Affiliation(s)
- Chiranjeet Saha
- Amity Institute of Biotechnology, Amity University, Kolkata, 700135, India
| | - Roumi Naskar
- Amity Institute of Biotechnology, Amity University, Kolkata, 700135, India
| | - Sandipan Chakraborty
- Center for Innovation in Molecular and Pharmaceutical Sciences (CIMPS), Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad, 500046, India
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Zerihun M, Qvit N. Selective inhibitors targeting Fis1/Mid51 protein-protein interactions protect against hypoxia-induced damage in cardiomyocytes. Front Pharmacol 2023; 14:1275370. [PMID: 38192411 PMCID: PMC10773907 DOI: 10.3389/fphar.2023.1275370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 11/27/2023] [Indexed: 01/10/2024] Open
Abstract
Cardiovascular diseases (CVDs) are the most common non-communicable diseases globally. An estimated 17.9 million people died from CVDs in 2019, representing 32% of all global deaths. Mitochondria play critical roles in cellular metabolic homeostasis, cell survival, and cell death, as well as producing most of the cell's energy. Protein-protein interactions (PPIs) have a significant role in physiological and pathological processes, and aberrant PPIs are associated with various diseases, therefore they are potential drug targets for a broad range of therapeutic areas. Due to their ability to mimic natural interaction motifs and cover relatively larger interaction region, peptides are very promising as PPI inhibitors. To expedite drug discovery, computational approaches are widely used for screening potential lead compounds. Here, we developed peptides that inhibit mitochondrial fission 1 (Fis1)/mitochondrial dynamics 51 kDa (Mid51) PPI to reduce the cellular damage that can lead to various human pathologies, such as CVDs. Based on a rational design approach we developed peptide inhibitors of the Fis1/Mid51 PPI. In silico and in vitro studies were done to evaluate the biological activity and molecular interactions of the peptides. Two peptides, CVP-241 and CVP-242 were identified based on low binding energy and molecular dynamics simulations. These peptides inhibit Fis1/Mid51 PPI (-1324.9 kcal mol-1) in docking calculations (CVP-241, -741.3 kcal mol-1, and CVP-242, -747.4 kcal mol-1), as well as in vitro experimental studies Fis1/Mid51 PPI (KD 0.054 µM) Fis1/Mid51 PPI + CVP-241 (KD 3.43 µM), and Fis1/Mid51 PPI + CVP-242 (KD 44.58 µM). Finally, these peptides have no toxicity to H9c2 cells, and they increase cell viability in cardiomyocytes (H9c2 cells). Consequently, the identified inhibitor peptides could serve as potent molecules in basic research and as leads for therapeutic development.
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Affiliation(s)
| | - Nir Qvit
- The Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, Israel
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Abedi Dorcheh F, Balmeh N, Hejazi SH, Allahyari Fard N. Investigation of the mutated antimicrobial peptides to inhibit ACE2, TMPRSS2 and GRP78 receptors of SARS-CoV-2 and angiotensin II type 1 receptor (AT1R) as well as controlling COVID-19 disease. J Biomol Struct Dyn 2023:1-24. [PMID: 38109185 DOI: 10.1080/07391102.2023.2292307] [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: 12/08/2022] [Accepted: 11/23/2023] [Indexed: 12/19/2023]
Abstract
SARS-CoV-2 is a global problem nowadays. Based on studies, some human receptors are involved in binding to SARS-CoV-2. Thus, the inhibition of these receptors can be effective in the treatment of Covid-19. Because of the proven benefits of antimicrobial peptides (AMPs) and the side effects of chemical drugs, they can be known as an alternative to recent medicines. RCSB PDB to obtain PDB id, StraPep and PhytAMP to acquire Bio-AMPs information and 3-D structure, and AlgPred, Toxinpred, TargetAntiAngio, IL-4pred, IL-6pred, ACPred and Hemopred databases were used to find the best score peptide features. HADDOCK 2.2 was used for molecular docking analysis, and UCSF Chimera software version 1.15, SWISS-MODEL and BIOVIA Discovery Studio Visualizer4.5 were used for mutation and structure modeling. Furthermore, MD simulation results were achieved from GROMACS 4.6.5. Based on the obtained results, the Moricin peptide was found to have the best affinity for ACE2. Moreover, Bacteriocin leucocin-A had the highest affinity for GRP78, Cathelicidin-6 had the best affinity for AT1R, and Bacteriocin PlnK had the best binding affinity for TMPRSS2. Additionally, Bacteriocin glycocin F, Bacteriocin lactococcin-G subunit beta and Cathelicidin-6 peptides were the most common compounds among the four receptors. However, these peptides also have some side effects. Consequently, the mutation eliminated the side effects, and MD simulation results indicated that the mutation proved the result of the docking analysis. The effect of AMPs on ACE2, GRP78, TMPRSS2 and AT1R receptors can be a novel treatment for Covid-19.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Fatemeh Abedi Dorcheh
- Department of Biotechnology, School of Bioscience and Biotechnology, Shahid Ashrafi Esfahani University of Isfahan, Sepahan Shahr, Iran
| | - Negar Balmeh
- Skin Diseases and Leishmaniasis Research Center, Department of Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Seyed Hossein Hejazi
- Skin Diseases and Leishmaniasis Research Center, Department of Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Najaf Allahyari Fard
- Department of Systems Biotechnology, National Institute of Genetic Engineering & Biotechnology (NIGEB), Tehran, Iran
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Harapan BN, Harapan T, Theodora L, Anantama NA. From Archipelago to Pandemic Battleground: Unveiling Indonesia's COVID-19 Crisis. J Epidemiol Glob Health 2023; 13:591-603. [PMID: 37707715 PMCID: PMC10686963 DOI: 10.1007/s44197-023-00148-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 08/25/2023] [Indexed: 09/15/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has posed unprecedented challenges to countries worldwide, including Indonesia. With its unique archipelagic geography consisting of more than 17,000 thousand islands, Indonesia faces unique complexities in managing the spread of the virus. Based on existing literature, this review article elaborates on key issues that have shaped Indonesia's COVID-19 response. The article begins by examining the early stages of the COVID-19 pandemic in Indonesia, along with the implementation of various preventive measures and the impact of the virus on public health. This article examines how Indonesia's socio-economic factors have generally influenced its healthcare system and further delves into the COVID-19 response strategies implemented by the Indonesian government and public health authorities as well as overall crisis preparedness. It discusses the actions taken to control the spread of the virus, including testing strategies and vaccination efforts. The difficulties encountered in implementing these measures are presented. In conclusion, this review article provides a comprehensive understanding of the COVID-19 crisis in Indonesia, covering facts on multiple dimensions ranging from the timeline of the pandemic to vaccination efforts, epidemiology, socio-economic implications, testing strategies, mobility patterns, public holidays, the impact of working from home, and the utilization of complementary and alternative medicine in addition to the standard of care for COVID-19. The insights gained from this article can complement future strategies for pandemic management and response in Indonesia and other countries facing similar challenges.
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Affiliation(s)
| | - Triswan Harapan
- Complementary Cardiovascular Clinic (CCV Clinic), Tangerang Selatan, Indonesia
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12
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Chinnadurai RK, Ponne S, Chitra L, Kumar R, Thayumanavan P, Subramanian B. Pharmacoinformatic approach to identify potential phytochemicals against SARS-CoV-2 spike receptor-binding domain in native and variants of concern. Mol Divers 2023; 27:2741-2766. [PMID: 36547813 PMCID: PMC9773690 DOI: 10.1007/s11030-022-10580-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 11/24/2022] [Indexed: 12/24/2022]
Abstract
Severe acute respiratory syndrome-related coronavirus-2 (SARS-CoV-2) pathogenesis is initiated by the binding of SARS-CoV-2 spike (S) protein with the angiotensin-converting enzyme 2 receptor (ACE2R) on the host cell surface. The receptor-binding domain (RBD) of the S protein mediates the binding and is more prone to mutations resulting in the generation of different variants. Recently, molecules with the potential to inhibit the interaction of S protein with ACE2R have been of interest due to their therapeutic value. In this context, the present work was performed to identify potential RBD binders from the Indian medicinal plant's phytochemical database through virtual screening, molecular docking, and molecular dynamic simulation. Briefly, 1578 compounds filtered from 9596 phytochemicals were chosen for screening against the RBD of the native SARS-CoV-2 S protein. Based on the binding energy, the top 30 compounds were selected and re-docked individually against the native and five variants of concern (VOCs: alpha, beta, gamma, delta, and omicron) of SARS-CoV-2. Four phytochemicals, namely withanolide F, serotobenine, orobanchol, and gibberellin A51, were found to be potential RBD binders in native and all SARS-CoV-2 VOCs. Among the four, withanolide F exhibited lower binding energy (- 10.84 to - 8.56 kcal/mol) and better ligand efficiency (- 0.3 to - 0.25) against all forms of RBD and hence was subjected to a 100 ns MD simulation which confirmed its stringent binding to the RBDs in native and VOCs. The study prioritizes withanolide F as a prospective COVID-19 (Coronavirus disease) therapeutic agent based on the observations. It warrants deeper investigations into the four promising leads for understanding their precise therapeutic value.
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Affiliation(s)
- Raj Kumar Chinnadurai
- Mahatma Gandhi Medical Advanced Research Institute, Sri Balaji Vidhyapeeth (Deemed to be University), Pondicherry, 607402, India.
| | - Saravanaraman Ponne
- Department of Biotechnology, Pondicherry University, Pondicherry, 605014, India
| | - Loganathan Chitra
- Department of Biochemistry, Periyar University, Salem, Tamil Nadu, 636011, India
| | - Rajender Kumar
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, 106 91, Stockholm, Sweden
| | | | - Balanehru Subramanian
- School of Biological Sciences, Sri Balaji Vidhyapeeth (Deemed to be University), Pondicherry, 607402, India
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13
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Bharadwaj KK, Rabha B, Ahmad I, Mathew SP, Bhattacharjee CK, Jaganathan BG, Poddar S, Patel H, Subramaniyan V, Chinni SV, Ramachawolran G, Saleem R, Khalifa Ali EH, Abdel-Daim MM, Baishya D, Ghosh A. Rhamnetin, a nutraceutical flavonoid arrests cell cycle progression of human ovarian cancer (SKOV3) cells by inhibiting the histone deacetylase 2 protein. J Biomol Struct Dyn 2023:1-16. [PMID: 38014451 DOI: 10.1080/07391102.2023.2275187] [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: 06/12/2023] [Accepted: 10/20/2023] [Indexed: 11/29/2023]
Abstract
Overexpression of HDAC 2 promotes cell proliferation in ovarian cancer. HDAC 2 is involved in chromatin remodeling, transcriptional repression, and the formation of condensed chromatin structures. Targeting HDAC 2 presents a promising therapeutic approach for correcting cancer-associated epigenetic abnormalities. Consequently, HDAC 2 inhibitors have evolved as an attractive class of anti-cancer agents. This work intended to investigate the anti-cancer abilities and underlying molecular mechanisms of Rhamnetin in human epithelial ovarian carcinoma cells (SKOV3), which remain largely unexplored. We employed various in vitro methods, including MTT, apoptosis study, cell cycle analysis, fluorescence microscopy imaging, and in vitro enzymatic HDAC 2 protein inhibition, to examine the chemotherapeutic sensitivity of Rhamnetin in SKOV3 cells. Additionally, we conducted in silico studies using molecular docking, MD simulation, MM-GBSA, DFT, and pharmacokinetic analysis to investigate the binding interaction mechanism within Rhamnetin and HDAC 2, alongside the compound's prospective as a lead candidate. The in vitro assay confirmed the cytotoxic effects of Rhamnetin on SKOV3 cells, through its inhibition of HDAC 2 activity. Rhamnetin, a nutraceutical flavonoid, halted at the G1 phase of the cell cycle and triggered apoptosis in SKOV3 cells. Furthermore, computational studies provided additional evidence of its stable binding to the HDAC 2 protein's binding site cavity. Based on our findings, we conclude that Rhamnetin effectively promotes apoptosis and mitigates the proliferation of SKOV3 cells through HDAC 2 inhibition. These results highlight Rhamnetin as a potential lead compound, opening a new therapeutic strategy for human epithelial ovarian cancer.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Bijuli Rabha
- Department of Bioengineering and Technology, Gauhati University, Guwahati, Assam, India
| | - Iqrar Ahmad
- Department of Pharmaceutical Chemistry, Prof. Ravindra Nikam College of Pharmacy, Dhule, Maharashtra, India
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra, India
| | - Sam P Mathew
- Stem Cells and Cancer Biology Research Group, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | | | - Bithiah Grace Jaganathan
- Stem Cells and Cancer Biology Research Group, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
- Jyoti and Bhupat Mehta School of Health Sciences and Technology, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Snikdha Poddar
- Department of Bioengineering and Technology, Gauhati University, Guwahati, Assam, India
| | - Harun Patel
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra, India
| | - Vetriselvan Subramaniyan
- Pharmacology Unit, Jeffrey Cheah School of Medicine and Health Sciences, MONASH University, Selangor, Malaysia
| | - Suresh V Chinni
- Department of Biochemistry, Faculty of Medicine, Bioscience, and Nursing, MAHSA University, Jenjarom, Selangor, Malaysia
| | - Gobinath Ramachawolran
- Department of Foundation, RCSI & UCD Malaysia Campus, Georgetown, Pulau Pinang, Malaysia
| | - Rasha Saleem
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Al-Baha University, Al-Baha, Saudi Arabia
| | - Eman Hussain Khalifa Ali
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Al-Baha University, Al-Baha, Saudi Arabia
| | - Mohamed M Abdel-Daim
- Department of Pharmaceutical Sciences, Pharmacy Program, Batterjee Medical College, Jeddah, Saudi Arabia
- Pharmacology Department, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, Egypt
| | - Debabrat Baishya
- Department of Bioengineering and Technology, Gauhati University, Guwahati, Assam, India
| | - Arabinda Ghosh
- Department of Computational Biology and Biotechnology, Mahapurasha Srimanta Sankaradeva Viswavidyalaya, Guwahati, India
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14
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Sun J, Liu X, Zhang S, Li M, Zhang Q, Chen J. Molecular insights and optimization strategies for the competitive binding of engineered ACE2 proteins: a multiple replica molecular dynamics study. Phys Chem Chem Phys 2023; 25:28479-28496. [PMID: 37846774 DOI: 10.1039/d3cp03392a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) continues to spread globally, and rapid viral evolution and the emergence of new variants pose challenges to pandemic control. During infection, the spike protein of SARS-CoV-2 interacts with the human ACE2 protein via its receptor binding domain (RBD), and it is known that engineered forms of ACE2 can compete with wild-type (WT) ACE2 for binding to inhibit infection. Here, we conducted multiple replica molecular dynamics (MRMD) simulations to study the mechanisms of the engineered ACE2 variants 3N39 and 3N94 and provide directions for optimization. Our findings reveal that engineered ACE2 is notably more efficacious in systems that show weaker binding to WT ACE2 (i.e., WT and BA.1 RBD), but also faces immune escape as the virus evolves. Moreover, by modifying residue types near the binding interface, engineered ACE2 alters the electrostatic potential distribution and reconfigures the hydrogen bonding network, which results in modified binding to the RBD. However, this structural rearrangement does not occur in all RBD variants. In addition, we identified potentially engineerable beneficial residues and potentially engineerable detrimental residues in both ACE2 and RBD. Functional conservation can thus enable the optimization of these residues and improve the binding competitiveness of engineered ACE2, which therefore provides additional immune escape prevention. Finally, we conclude that these findings have implications for understanding the mechanisms responsible for engineered ACE2 and can help us to develop engineered ACE2 proteins that show superior performance.
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Affiliation(s)
- Jiahao Sun
- 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.
| | - Meng Li
- 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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15
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Al-Wahaibi LH, Rehman MT, Al-Saleem MSM, Basudan OA, El-Gamal AA, Abdelkader MSA, AlAjmi MF, Abdel-Mageed WM. Virtual screening and molecular dynamics simulation study of abyssomicins as potential inhibitors of COVID-19 virus main protease and spike protein. J Biomol Struct Dyn 2023; 41:8961-8977. [PMID: 36300522 DOI: 10.1080/07391102.2022.2139295] [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: 09/14/2022] [Accepted: 10/18/2022] [Indexed: 10/31/2022]
Abstract
The lack of any effective cure for the infectious COVID-19 disease has created a sense of urgency and motivated the search for effective antiviral drugs. Abyssomicins are actinomyces-derived spirotetronates polyketides antibiotics known for their promising antibacterial, antitumor, and antiviral activities. In this study, computational approaches were used to investigate the binding mechanism and the inhibitory ability of 38 abyssomicins against the main protease (Mpro) and the spike protein receptor-binding domain (RBD) of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). The results identified abyssomicins C, J, W, atrop-O-benzyl abyssomicin C, and atrop-O-benzyl desmethyl abyssomicin C as the most potential inhibitors of Mpro and RBD with binding energy ranges between -8.1 and -9.9 kcal mol-1; and between -6.9 and -8.2 kcal mol-1, respectively. Further analyses of physicochemical properties and drug-likeness suggested that all selected active abyssomicins, with the exception of abyssomicin J, obeyed Lipinski's rule of five. The stability of protein-ligand complexes was confirmed by performing molecular dynamics simulation for 100 ns and evaluating parameters such as such as root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), solvent accessible surface area (SASA), total number of contacts, and secondary structure. Prime/MM-GBSA (Molecular Mechanics-General Born Surface Area) and principal component analysis (PCA) analyses also confirmed the stable nature of protein-ligand complexes. Overall, the results showed that the studied abyssomicins have significant interactions with the selected protein targets; therefore, they were deemed viable candidates for further in vitro and in vivo evaluation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Lamya H Al-Wahaibi
- Department of Chemistry, Science College, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Md Tabish Rehman
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Muneera S M Al-Saleem
- Department of Chemistry, Science College, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Omer A Basudan
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Ali A El-Gamal
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
- Pharmacognosy Department, Faculty of Pharmacy, Mansoura University, El Mansoura, Egypt
| | | | - Mohamed F AlAjmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Wael M Abdel-Mageed
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
- Pharmacognosy Department, Faculty of Pharmacy, Assiut University, Assiut, Egypt
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16
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Mahajan S, Bisht MS, Chakraborty A, Sharma VK. Genome of Phyllanthus emblica: the medicinal plant Amla with super antioxidant properties. FRONTIERS IN PLANT SCIENCE 2023; 14:1210078. [PMID: 37727852 PMCID: PMC10505619 DOI: 10.3389/fpls.2023.1210078] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 08/15/2023] [Indexed: 09/21/2023]
Abstract
Phyllanthus emblica or Indian gooseberry, commonly known as amla, is an important medicinal horticultural plant used in traditional and modern medicines. It bears stone fruits with immense antioxidant properties due to being one of the richest natural sources of vitamin C and numerous flavonoids. This study presents the first genome sequencing of this species performed using 10x Genomics and Oxford Nanopore Technology. The draft genome assembly was 519 Mbp in size and consisted of 4,384 contigs, N50 of 597 Kbp, 98.4% BUSCO score, and 37,858 coding sequences. This study also reports the genome-wide phylogeny of this species with 26 other plant species that resolved the phylogenetic position of P. emblica. The presence of three ascorbate biosynthesis pathways including L-galactose, galacturonate, and myo-inositol pathways was confirmed in this genome. A comprehensive comparative evolutionary genomic analysis including gene family expansion/contraction and identification of multiple signatures of adaptive evolution provided evolutionary insights into ascorbate and flavonoid biosynthesis pathways and stone fruit formation through lignin biosynthesis. The availability of this genome will be beneficial for its horticultural, medicinal, dietary, and cosmetic applications and will also help in comparative genomics analysis studies.
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Affiliation(s)
| | | | | | - Vineet K. Sharma
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh, India
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Sekaran K, Karthik A, Varghese RP, Sathiyarajeswaran P, Shree Devi MS, Siva R, George Priya Doss C. In silico network pharmacology study on Glycyrrhiza glabra: Analyzing the immune-boosting phytochemical properties of Siddha medicinal plant against COVID-19. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 138:233-255. [PMID: 38220426 PMCID: PMC10275734 DOI: 10.1016/bs.apcsb.2023.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
Immunosenescence is a pertinent factor in the mortality rate caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). The changes in the immune system are strongly associated with age and provoke the deterioration of the individual's health. Traditional medical practices in ancient India effectively deal with COVID-19 by boosting natural immunity through medicinal plants. The anti-inflammatory and antiviral properties of Glycyrrhiza glabra are potent in fighting against COVID-19 and promote immunity boost against the severity of the infection. Athimadhura Chooranam, a polyherbal formulation containing Glycyrrhiza glabra as the main ingredient, is recommended as an antiviral Siddha herb by the Ministry of AYUSH. This paper is intended to identify the phytoconstituents of Glycyrrhiza glabra that are actively involved in preventing individuals from COVID-19 transmission. The modulated pathways, enrichment study, and drug-likeness are calculated from the target proteins of the phytoconstituents at the pharmacological activity (Pa) of more than 0.7. Liquiritigenin and Isoliquiritin, the natural compounds in Glycyrrhiza glabra, belong to the flavonoid class and exhibit ameliorative effects against COVID-19. The latter compound displays a higher protein interaction to a maximum of six, out of which HMOX1, PLAU, and PGR are top-hub genes. ADMET screening further confirms the significance of the abovementioned components containing better drug-likeness. The molecular docking and molecular dynamics method identified liquiritigenin as a possible lead molecule capable of inhibiting the activity of the major protease protein of SARS-CoV-2. The findings emphasize the importance of in silico network pharmacological assessments in delivering cost-effective, time-bound clinical drugs.
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Affiliation(s)
- Karthik Sekaran
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Ashwini Karthik
- Department of Biology, Mount Carmel College Autonomous, Bengaluru, India
| | | | | | | | - R Siva
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - C George Priya Doss
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India.
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18
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Upadhyay R, Tiwari KN. The antiviral potential of Phyllanthus species: a systematic review. Arch Virol 2023; 168:177. [PMID: 37310509 DOI: 10.1007/s00705-023-05802-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 04/17/2023] [Indexed: 06/14/2023]
Abstract
Viral infections and diseases caused by viruses are worldwide problems. According to a WHO report, three to five million people are chronically infected with hepatitis B virus (HBV), hepatitis C virus (HCV), and human immunodeficiency virus (HIV) each year globally. Since some viruses mutate very quickly, developing antiviral drugs can be a daunting task. Moreover, currently used synthetic drugs are toxic and associated with side effects. Therefore, there is a need to search for alternative natural remedies that have low toxicity, a new mechanism of action, and no major side effects. Phyllanthus plants have traditionally been used to treat viral hepatitis and liver damage in many tropical and subtropical countries worldwide. In this review, we discuss the therapeutic potential of Phyllanthus spp. against HBV, HCV, HIV, herpes simplex virus, and SARS-CoV-2. The inferences from in vitro and in vivo studies and clinical trials validate the use of Phyllanthus in antiviral remedies.
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Affiliation(s)
- Richa Upadhyay
- Department of Botany, Mihir Bhoj PG College, Dadri, G.B. Nagar, 203207, Uttar Pradesh, India
| | - Kavindra Nath Tiwari
- Department of Botany, MMV, Banaras Hindu University, Varanasi, 221005, Uttar Pradesh, India.
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Tassakka ACMAR, Iskandar IW, Alam JF, Permana AD, Massi MN, Jompa J, Liao LM. Docking Studies and Molecular Dynamics Simulations of Potential Inhibitors from the Brown Seaweed Sargassum polycystum (Phaeophyceae) against PLpro of SARS-CoV-2. BIOTECH 2023; 12:46. [PMID: 37366794 DOI: 10.3390/biotech12020046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/01/2023] [Accepted: 06/05/2023] [Indexed: 06/28/2023] Open
Abstract
The COVID-19 disease is a major problem affecting human health all over the world. Consequently, researchers have been trying to find solutions to treat this pandemic-scale disease. Even if there are vaccines and approved drugs that could decrease the spread of this pandemic, multidisciplinary approaches are still needed to identify new small molecules as alternatives to combat COVID-19, especially those from nature. In this study, we employed computational approaches by screening 17 natural compounds from the tropical brown seaweed Sargassum polycystum known to have anti-viral properties that benefit human health. This study assessed some seaweed natural products that are bound to the PLpro of SARS-CoV-2. By employing pharmacophore and molecular docking, these natural compounds from S. polycystum showed remarkable scores for protein targets with competitive scores compared to X-ray crystallography ligands and well-known antiviral compounds. This study provides insightful information for advanced study and further in vitro examination and clinical investigation for drug development prospects of abundant yet underexploited tropical seaweeds.
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Affiliation(s)
| | | | - Jamaluddin Fitrah Alam
- Faculty of Marine Science and Fisheries, Universitas Hasanuddin, Makassar 90245, Indonesia
| | - Andi Dian Permana
- Faculty of Pharmacy, Universitas Hasanuddin, Makassar 90245, Indonesia
| | | | - Jamaluddin Jompa
- Faculty of Marine Science and Fisheries, Universitas Hasanuddin, Makassar 90245, Indonesia
| | - Lawrence Manzano Liao
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8528, Japan
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20
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Gosu V, Sasidharan S, Saudagar P, Radhakrishnan K, Lee HK, Shin D. Deciphering the intrinsic dynamics of unphosphorylated IRAK4 kinase bound to type I and type II inhibitors. Comput Biol Med 2023; 160:106978. [DOI: https:/doi.org/10.1016/j.compbiomed.2023.106978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/18/2023]
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21
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Patel U, Desai K, Dabhi RC, Maru JJ, Shrivastav PS. Bioprospecting phytochemicals of Rosmarinus officinalis L. for targeting SARS-CoV-2 main protease (M pro): a computational study. J Mol Model 2023; 29:161. [PMID: 37115321 PMCID: PMC10141822 DOI: 10.1007/s00894-023-05569-6] [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: 09/24/2022] [Accepted: 04/21/2023] [Indexed: 04/29/2023]
Abstract
CONTEXT The persistent spread of highly contagious COVID-19 disease is one of the deadliest occurrences in the history of mankind. Despite the distribution of numerous efficacious vaccines and their extensive usage, the perpetual effectiveness of immunization is being catechized. Therefore, discovering an alternative therapy to control and prevent COVID-19 infections has become a top priority. The main protease (Mpro) plays a key role in viral replication, making it an intriguing pharmacological target for SARS-CoV-2. METHODS In this context, virtual screening of thirteen bioactive polyphenols and terpenoids of Rosmarinus officinalis L. was performed using several computational modules including molecular docking, ADMET, drug-likeness characteristics, and molecular dynamic simulation to predict the potential inhibitors against SARS-CoV-2 Mpro (PDB: 6LU7). The results suggest that apigenin, betulinic acid, luteolin, carnosol, and rosmarinic acid may emerge as potential inhibitors of SARS-CoV-2 with acceptable drug-likeness, pharmacokinetics, ADMET characteristics, and binding interactions comparable with remdesivir and favipiravir. These findings imply that some of the active components of Rosmarinus officinalis L. can serve as an effective antiviral source for the development of therapeutics for SARS-CoV-2 infection.
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Affiliation(s)
- Unnati Patel
- Department of Chemistry, University School of Sciences, Gujarat University, Ahmedabad, 380009, India
| | - Krishna Desai
- Department of Botany, Bioinformatics and Climate Change Impacts Management, University School of Sciences, Gujarat University, Ahmedabad, 380009, India
| | - Ranjitsinh C Dabhi
- Department of Chemistry, University School of Sciences, Gujarat University, Ahmedabad, 380009, India
| | - Jayesh J Maru
- Department of Chemistry, University School of Sciences, Gujarat University, Ahmedabad, 380009, India
| | - Pranav S Shrivastav
- Department of Chemistry, University School of Sciences, Gujarat University, Ahmedabad, 380009, India.
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22
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Gosu V, Sasidharan S, Saudagar P, Radhakrishnan K, Lee HK, Shin D. Deciphering the intrinsic dynamics of unphosphorylated IRAK4 kinase bound to type I and type II inhibitors. Comput Biol Med 2023; 160:106978. [PMID: 37172355 DOI: 10.1016/j.compbiomed.2023.106978] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 04/07/2023] [Accepted: 04/23/2023] [Indexed: 05/14/2023]
Abstract
Interleukin-1 receptor-associated kinase 4 (IRAK4) is a vital protein involved in Toll-like and interleukin-1 receptor signal transduction. Several studies have reported regarding the crystal structure, dynamic properties, and interactions with inhibitors of the phosphorylated form of IRAK4. However, no dynamic properties of inhibitor-bound unphosphorylated IRAK4 have been previously studied. Herein, we report the intrinsic dynamics of unphosphorylated IRAK4 (uIRAK4) bound to type I and type II inhibitors. The corresponding apo and inhibitor-bound forms of uIRAK4 were subjected to three independent simulations of 500 ns (total 1.5 μs) each, and their trajectories were analyzed. The results indicated that all three systems were relatively stable, except for the type II inhibitor-bound form of uIRAK4, which exhibited less compact folding and higher solvent surface area. The intra-hydrogen bonds corroborated the structural deformation of the type-II inhibitor-bound complex, which could be attributed to the long molecular structure of the type-II inhibitor. Moreover, the type II inhibitor bound to uIRAK4 showed higher binding free energy with uIRAK4 than the type I inhibitor. The free energy landscape analysis showed a reorientation of Phe330 side chain from the DFG motif at different metastable states for all the systems. The intra-residual distance between residues Lys213, Glu233, Tyr262, and Phe330 suggests a functional interplay when the inhibitors are bound to uIRAK4, thereby hinting at their crucial role in the inhibition mechanism. Ultimately, the intrinsic dynamics study observed between type I/II inhibitor-bound forms of uIRAK4 may assist in better understanding the enzyme and designing therapeutic compounds.
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Affiliation(s)
- Vijayakumar Gosu
- Department of Animal Biotechnology, Jeonbuk National University, Jeonju, 54896, Republic of Korea
| | - Santanu Sasidharan
- Department of Biotechnology, National Institute of Technology, Warangal, Telangana, 506004, India
| | - Prakash Saudagar
- Department of Biotechnology, National Institute of Technology, Warangal, Telangana, 506004, India
| | - Kamalakannan Radhakrishnan
- Combinatorial Tumor Immunotherapy MRC, Chonnam National University Medical School, Hwasun-gun, Jeonnam, 58128, Republic of Korea
| | - Hak-Kyo Lee
- Department of Animal Biotechnology, Jeonbuk National University, Jeonju, 54896, Republic of Korea; Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju, 54896, Republic of Korea.
| | - Donghyun Shin
- Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju, 54896, Republic of Korea.
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23
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Das K, Das P, Almuqbil M, Asdaq SMB, Nikhil K, Preethi K, Angelinkiruba A, Alomar NF, Al Harbi RM, Al Abdullah WA, Alshehri SM, Laghabi YA, Alsaegh AR, Mohzari Y, Alshehri S, Mannasaheb BA, Rabbani SI. Inhibition of SARS-CoV2 viral infection with natural antiviral plants constituents: An in-silico approach. JOURNAL OF KING SAUD UNIVERSITY. SCIENCE 2023; 35:102534. [PMID: 36619666 PMCID: PMC9811905 DOI: 10.1016/j.jksus.2022.102534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 12/01/2022] [Accepted: 12/29/2022] [Indexed: 05/28/2023]
Abstract
Background and Objective In 2019, a novel coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS CoV-2) was declared pandemic. Advancement in computational technology has provided rapid and cost-effective techniques to test the efficacy of newer therapeutic agents. This study evaluated some of the potent phytochemicals obtained from AYUSH (Ayurveda, Yoga, Naturopathy, Unani, Siddha, Sowa-Rigpa, and Homeopathy)-listed medicinal plants against SARS-CoV-2 proteins using computational techniques. Materials and methods The potential SARS-CoV-2 protein targets were utilized to study the ligand-protein binding characteristics. The bioactive agents were obtained from ashwagandha, liquorice, amla, neem, tinospora, pepper, and stevia. Ivermectin was utilized as a reference agent to compare its efficacy with phytochemicals. Results The computational analysis suggested that all the bioactive components from the selected plants possessed negative docking scores (ranging from -6.24 to -10.53). The phytoconstituents were well absorbed, distributed in the body except for the CNS, metabolized by liver enzymes, well cleared from the body, and well tolerated. The data suggest that AYUSH-recommended plants demonstrated therapeutic efficacy against SARS CoV-2 virus infection with significantly reduced toxicity. Conclusion The phytoconstituents were found to hinder the early stages of infection, such as absorption and penetration, while ivermectin prevented the passage of genetic material from the cytoplasm to the nucleus. Additional research involving living tissues and clinical trials are suggested to corroborate the computational findings.
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Affiliation(s)
- Kuntal Das
- NITTE College of Pharmacy, Yelahanka, Bangalore 560064, India
| | - Paramita Das
- Krupanidhi College of Pharmacy, #12/1, Chikkabelandur, Carmelaram Post, Varthur Hobli, Bangalore 560035, India
| | - Mansour Almuqbil
- Department of Clinical Pharmacy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | | | - K Nikhil
- Krupanidhi College of Pharmacy, #12/1, Chikkabelandur, Carmelaram Post, Varthur Hobli, Bangalore 560035, India
| | - K Preethi
- Krupanidhi College of Pharmacy, #12/1, Chikkabelandur, Carmelaram Post, Varthur Hobli, Bangalore 560035, India
| | - A Angelinkiruba
- Krupanidhi College of Pharmacy, #12/1, Chikkabelandur, Carmelaram Post, Varthur Hobli, Bangalore 560035, India
| | | | - Rawabi M Al Harbi
- Pharmaceutical Services, King Saud Medical City, Riyadh, Saudi Arabia
| | | | - Sami M Alshehri
- Pharmaceutical Services, King Saud Medical City, Riyadh, Saudi Arabia
| | - Yahya A Laghabi
- Pharmaceutical Services, King Saud Medical City, Riyadh, Saudi Arabia
| | - Ahmed R Alsaegh
- Clinical Pharmacy Department, King Saud Medical City, Riyadh, Saudi Arabia
| | - Yahya Mohzari
- Clinical Pharmacy Department, King Saud Medical City, Riyadh, Saudi Arabia
| | - Sultan Alshehri
- Department of Pharmaceutical Sciences, College of Pharmacy, AlMaarefa University, Ad Diriyah 13713, Saudi Arabia
| | | | - Syed Imam Rabbani
- Department of Pharmacology and Toxicology, College of Pharmacy, Qassim University, Buraydah 51452, Saudi Arabia
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24
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Identification of medicinal plant-based phytochemicals as a potential inhibitor for SARS-CoV-2 main protease (M pro) using molecular docking and deep learning methods. Comput Biol Med 2023; 157:106785. [PMID: 36931201 PMCID: PMC10008098 DOI: 10.1016/j.compbiomed.2023.106785] [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: 11/19/2022] [Revised: 02/15/2023] [Accepted: 03/10/2023] [Indexed: 03/14/2023]
Abstract
Highly transmissive and rapidly evolving Coronavirus disease-2019 (COVID-19), a viral disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), triggered a global pandemic, which is one of the most researched viruses in the academia. Effective drugs to treat people with COVID-19 have yet to be developed to reduce mortality and transmission. Studies on the SARS-CoV-2 virus identified that its main protease (Mpro) might be a potential therapeutic target for drug development, as this enzyme plays a key role in viral replication. In search of potential inhibitors of Mpro, we developed a phytochemical library consisting of 2431 phytochemicals from 104 Korean medicinal plants that exhibited medicinal and antioxidant properties. The library was screened by molecular docking, followed by revalidation by re-screening with a deep learning method. Recurrent Neural Networks (RNN) computing system was used to develop an inhibitory predictive model using SARS coronavirus Mpro dataset. It was deployed to screen the top 12 compounds based on their docked binding affinity that ranged from -8.0 to -8.9 kcal/mol. The top two lead compounds, Catechin gallate and Quercetin 3-O-malonylglucoside, were selected depending on inhibitory potency against Mpro. Interactions with the target protein active sites, including His41, Met49, Cys145, Met165, and Thr190 were also examined. Molecular dynamics simulation was performed to analyze root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (RG), solvent accessible surface area (SASA), and number of hydrogen bonds. Results confirmed the inflexible nature of the docked complexes. Absorption, distribution, metabolism, excretion, and toxicity (ADMET), as well as bioactivity prediction confirmed the pharmaceutical activities of the lead compound. Findings of this research might help scientists to optimize compatible drugs for the treatment of COVID-19 patients.
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25
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Babaoglu ZY, Kilic D. Virtual screening, molecular simulations and bioassays: Discovering novel microsomal prostaglandin E Synthase-1 (mPGES-1) inhibitors. Comput Biol Med 2023; 155:106616. [PMID: 36780799 DOI: 10.1016/j.compbiomed.2023.106616] [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: 06/14/2022] [Revised: 01/05/2023] [Accepted: 01/28/2023] [Indexed: 02/05/2023]
Abstract
Microsomal prostaglandin E synthase-1 (mPGES-1) is an inducible prostaglandin E synthase expressed following exposure to pro-inflammatory stimuli. The mPGES-1 enzyme represents a new target for the therapeutic treatment of acute and chronic inflammatory disorders and cancer. In the present study, compounds from the ZINC15 database with an indole scaffold were docked at the mPGES-1 binding site using Glide (high-throughput virtual screening [HTVS], standard precision [SP] and extra precision [XP]), and the stabilities of the complexes were determined by molecular simulation studies. Following HTVS, the top 10% compounds were retained and further screened by SP. Again, the top 10% of these compounds were retained. Finally, the Glide XP scores of the compounds were determined, 20% were analyzed, and the Prime MM-GBSA total free binding energies of the compounds were calculated. The molecular simulations (100 ns) of the reference ligand, LVJ, and the two best-scoring compounds were performed with the Desmond program to analyze the dynamics of the target protein-ligand complexes. In human lung cells treated with the hit compounds, cell viability by colorimetric method and PGE2 levels by immunoassay method were determined. These in vitro experiments demonstrated that the two indole-containing hit compounds are potential novel inhibitors of mPGES-1 and are, therefore, potential therapeutic agents for cancer/inflammation therapies. Moreover, the compounds are promising lead mPGES-1 inhibitors for novel molecule design.
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Affiliation(s)
| | - Deryanur Kilic
- Department of Chemistry, Faculty of Science, Atatürk University, Erzurum, Turkey.
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26
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Design, synthesis and anti-cancer evaluation of genistein-1,3,5-triazine derivatives. Tetrahedron 2023. [DOI: 10.1016/j.tet.2023.133293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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27
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Zou J, Qian J, Liu S, Li R, Zhang X, Yang S, Liu Y, Liu W, Ma S, Shi D. Design, Synthesis, Biological Evaluation and Molecular Dynamics Simulations Study of Genistein‐
O
‐1,3,5‐Triazine Derivatives as Multifunctional Anti‐Alzheimer Agents. ChemistrySelect 2022. [DOI: 10.1002/slct.202203997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Jing‐Pei Zou
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University/Jiangsu Key Laboratory of Marine Bioresources and environment, School of Pharmacy Jiangsu Ocean University Lianyungang 222005 People's Republic of China
| | - Jing‐Jing Qian
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University/Jiangsu Key Laboratory of Marine Bioresources and environment, School of Pharmacy Jiangsu Ocean University Lianyungang 222005 People's Republic of China
| | - Shan‐Ming Liu
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University/Jiangsu Key Laboratory of Marine Bioresources and environment, School of Pharmacy Jiangsu Ocean University Lianyungang 222005 People's Republic of China
| | - Rui Li
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University/Jiangsu Key Laboratory of Marine Bioresources and environment, School of Pharmacy Jiangsu Ocean University Lianyungang 222005 People's Republic of China
| | - Xiao‐Qing Zhang
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University/Jiangsu Key Laboratory of Marine Bioresources and environment, School of Pharmacy Jiangsu Ocean University Lianyungang 222005 People's Republic of China
| | - Shun Yang
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University/Jiangsu Key Laboratory of Marine Bioresources and environment, School of Pharmacy Jiangsu Ocean University Lianyungang 222005 People's Republic of China
| | - Yu‐Wei Liu
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University/Jiangsu Key Laboratory of Marine Bioresources and environment, School of Pharmacy Jiangsu Ocean University Lianyungang 222005 People's Republic of China
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology Lianyungang 222005 People's Republic of China
| | - Wei‐Wei Liu
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University/Jiangsu Key Laboratory of Marine Bioresources and environment, School of Pharmacy Jiangsu Ocean University Lianyungang 222005 People's Republic of China
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology Lianyungang 222005 People's Republic of China
| | - Shao‐Jie Ma
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University/Jiangsu Key Laboratory of Marine Bioresources and environment, School of Pharmacy Jiangsu Ocean University Lianyungang 222005 People's Republic of China
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology Lianyungang 222005 People's Republic of China
| | - Da‐Hua Shi
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University/Jiangsu Key Laboratory of Marine Bioresources and environment, School of Pharmacy Jiangsu Ocean University Lianyungang 222005 People's Republic of China
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology Lianyungang 222005 People's Republic of China
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28
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Gumede NJ. Pathfinder-Driven Chemical Space Exploration and Multiparameter Optimization in Tandem with Glide/IFD and QSAR-Based Active Learning Approach to Prioritize Design Ideas for FEP+ Calculations of SARS-CoV-2 PL pro Inhibitors. Molecules 2022; 27:8569. [PMID: 36500659 PMCID: PMC9741453 DOI: 10.3390/molecules27238569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 11/25/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
A global pandemic caused by the SARS-CoV-2 virus that started in 2020 and has wreaked havoc on humanity still ravages up until now. As a result, the negative impact of travel restrictions and lockdowns has underscored the importance of our preparedness for future pandemics. The main thrust of this work was based on addressing this need by traversing chemical space to design inhibitors that target the SARS-CoV-2 papain-like protease (PLpro). Pathfinder-based retrosynthesis analysis was used to generate analogs of GRL-0617 using commercially available building blocks by replacing the naphthalene moiety. A total of 10 models were built using active learning QSAR, which achieved good statistical results such as an R2 > 0.70, Q2 > 0.64, STD Dev < 0.30, and RMSE < 0.31, on average for all models. A total of 35 ideas were further prioritized for FEP+ calculations. The FEP+ results revealed that compound 45 was the most active compound in this series with a ΔG of −7.28 ± 0.96 kcal/mol. Compound 5 exhibited a ΔG of −6.78 ± 1.30 kcal/mol. The inactive compounds in this series were compound 91 and compound 23 with a ΔG of −5.74 ± 1.06 and −3.11 ± 1.45 kcal/mol. The combined strategy employed here is envisaged to be of great utility in multiparameter lead optimization efforts, to traverse chemical space, maintaining and/or improving the potency as well as the property space of synthetically aware design ideas.
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Affiliation(s)
- Njabulo Joyfull Gumede
- Department of Chemistry, Mangosuthu University of Technology, P.O. Box 12363, Jacobs 4026, South Africa
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29
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Patel CN, Jani SP, Prasanth Kumar S, Modi KM, Kumar Y. Computational investigation of natural compounds as potential main protease (M pro) inhibitors for SARS-CoV-2 virus. Comput Biol Med 2022; 151:106318. [PMID: 36423529 PMCID: PMC9673090 DOI: 10.1016/j.compbiomed.2022.106318] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 11/05/2022] [Accepted: 11/13/2022] [Indexed: 11/19/2022]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is significantly impacting human lives, overburdening the healthcare system and weakening global economies. Plant-derived natural compounds are being largely tested for their efficacy against COVID-19 targets to combat SARS-CoV-2 infection. The SARS-CoV-2 Main protease (Mpro) is considered an appealing target because of its role in replication in host cells. We curated a set of 7809 natural compounds by combining the collections of five databases viz Dr Duke's Phytochemical and Ethnobotanical database, IMPPAT, PhytoHub, AromaDb and Zinc. We applied a rigorous computational approach to identify lead molecules from our curated compound set using docking, dynamic simulations, the free energy of binding and DFT calculations. Theaflavin and ginkgetin have emerged as better molecules with a similar inhibition profile in both SARS-CoV-2 and Omicron variants.
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Affiliation(s)
- Chirag N Patel
- Computer-Aided Drug Design Group, Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institute of Health, Frederick, MD, 21702, USA; Department of Botany, Bioinformatics, and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India.
| | - Siddhi P Jani
- Institute of Science, Nirma University, Ahmedabad, 382481, Gujarat, India
| | - Sivakumar Prasanth Kumar
- Department of Botany, Bioinformatics, and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India
| | - Krunal M Modi
- Department of Molecular Electrochemistry and Catalysis, J. Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejskova 2155/3, 182 23 Prague 8, Czech Republic; Department of Humanities and Science, School of Engineering, Indrashil University, Mehsana, 382740, Gujarat, India.
| | - Yogesh Kumar
- Department of General Visceral and Thoracic Surgery, University Medical Center Hamburg- Eppendorf, Martinistrasse 52, Hamburg, 20246, Germany
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30
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Chang SN, Keretsu S, Kang SC. Evaluation of decursin and its isomer decursinol angelate as potential inhibitors of human glutamate dehydrogenase activity through in silico and enzymatic assay screening. Comput Biol Med 2022; 151:106287. [PMID: 36455296 DOI: 10.1016/j.compbiomed.2022.106287] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 10/09/2022] [Accepted: 11/06/2022] [Indexed: 11/16/2022]
Abstract
Glutaminolysis is a typical hallmark of malignant tumors across different cancers. Glutamate dehydrogenase (GDH, GLUD1) is one such enzyme involved in the conversion of glutamate to α-ketoglutarate. High levels of GDH are associated with numerous diseases and is also a prognostic marker for predicting metastasis in colorectal cancer. Therefore, inhibiting GDH can be a crucial therapeutic target. Here in this study, we performed molecular docking analysis of 8 different plants derived single compounds collected from pubChem database for screening and selected decursin (DN) and decursinol angelate (DA). We performed molecular dynamics simulation (MD), monitored the stability, interaction for protein and docked ligand at 50 ns, and evaluated the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) free energy calculation on the twoselected compounds along with a standard inhibitor epigallocatechin gallate (EGCG) as reference. The final results showed the formation of stable hydrogen bond interactions by DN and DA in the residues of R400 and Y386 at the ADP activation site of GDH, which was important for the selective inhibition of GDH activity. Additionally, the total binding energy of DN and DA were -115.5 kJ/mol and -106.2 kJ/mol, which was higher than the standard reference GDH inhibitor EGCG (-92.8 kJ/mol). Furthermore, biochemical analysis for GDH inhibition substantiated our computational results and established DN and DA as novel GDH inhibitor. The percentage of IC50 inhibition for DN and DA were 1.035 μM and 1.432 μM. Conclusively, DN and DA can be a novel therapeutic drug for inhibition of glutamate dehydrogenase.
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Affiliation(s)
| | - Seketoulie Keretsu
- Department of Pathology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Sun Chul Kang
- Department of Biotechnology, Daegu University, Gyeongsan, 38453, South Korea.
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31
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Singh MB, Sharma R, Kumar D, Khanna P, Mansi, Khanna L, Kumar V, Kumari K, Gupta A, Chaudhary P, Kaushik N, Choi EH, Kaushik NK, Singh P. An understanding of coronavirus and exploring the molecular dynamics simulations to find promising candidates against the Mpro of nCoV to combat the COVID-19: A systematic review. J Infect Public Health 2022; 15:1326-1349. [PMID: 36288640 PMCID: PMC9579205 DOI: 10.1016/j.jiph.2022.10.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 10/08/2022] [Accepted: 10/12/2022] [Indexed: 11/10/2022] Open
Abstract
The first infection case of new coronavirus was reported at the end of 2019 and after then, the cases are reported in all nations across the world in a very short period. Further, the regular news of mutations in the virus has made life restricted with appropriate behavior. To date, a new strain (Omicron and its new subvariant Omicron XE) has brought fear amongst us due to a higher trajectory of increase in the number of cases. The researchers thus started giving attention to this viral infection and discovering drug-like candidates to cure the infections. Finding a drug for any viral infection is not an easy task and takes plenty of time. Therefore, computational chemistry/bioinformatics is followed to get promising molecules against viral infection. Molecular dynamics (MD) simulations are being explored to get drug candidates in a short period. The molecules are screened via molecular docking, which provides preliminary information which can be further verified by molecular dynamics (MD) simulations. To understand the change in structure, MD simulations generated several trajectories such as root mean square deviation (RMSD), root mean square fluctuation (RMSF), hydrogen bonding, and radius of gyration for the main protease (Mpro) of the new coronavirus (nCoV) in the presence of small molecules. Additionally, change in free energy for the formation of complex of Mpro of nCoV with the small molecule can be determined by applying molecular mechanics with generalized born and surface area solvation (MM-GBSA). Thus, the promising molecules can be further explored for clinical trials to combat coronavirus disease-19 (COVID-19).
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Affiliation(s)
- Madhur Babu Singh
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, New Delhi, India
| | - Ritika Sharma
- Department of Biochemistry, University of Delhi, New Delhi, India
| | - Durgesh Kumar
- Department of Chemistry, Maitreyi College, University of Delhi, Delhi, India
| | - Pankaj Khanna
- Department of Chemistry, Acharya Narendra Dev College, University of Delhi, New Delhi, India
| | - Mansi
- University School of Basic and Applied Sciences, Guru Gobind Singh Indraprastha University, New Delhi, India
| | - Leena Khanna
- University School of Basic and Applied Sciences, Guru Gobind Singh Indraprastha University, New Delhi, India
| | - Vinod Kumar
- Special Centre for Nanoscience (SCNS), Jawaharlal Nehru University, New Delhi, India
| | - Kamlesh Kumari
- Department of Zoology, University of Delhi, New Delhi, India
| | - Akanksha Gupta
- Department of Chemistry, Sri Venkateswara College, University of Delhi, New Delhi, India
| | - Preeti Chaudhary
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, New Delhi, India
| | - Neha Kaushik
- Department of Biotechnology, College of Engineering, The University of Suwon, Hwaseong-si 18323, Republic of Korea.
| | - Eun Ha Choi
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, Republic of Korea
| | - Nagendra Kumar Kaushik
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, Republic of Korea.
| | - Prashant Singh
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, New Delhi, India.
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Dey R, Samadder A, Nandi S. Exploring the Targets of Novel Corona Virus and Docking-based Screening of Potential Natural Inhibitors to Combat COVID-19. Curr Top Med Chem 2022; 22:2410-2434. [PMID: 36281864 DOI: 10.2174/1568026623666221020163831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 09/07/2022] [Accepted: 09/21/2022] [Indexed: 01/20/2023]
Abstract
There is a need to explore natural compounds against COVID-19 due to their multitargeted actions against various targets of nCoV. They act on multiple sites rather than single targets against several diseases. Thus, there is a possibility that natural resources can be repurposed to combat COVID-19. However, the biochemical mechanisms of these inhibitors were not known. To reveal the mode of anti-nCoV action, structure-based docking plays a major role. The present study is an attempt to explore various potential targets of SARS-CoV-2 and the structure-based screening of various potential natural inhibitors to combat the novel coronavirus.
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Affiliation(s)
- Rishita Dey
- Department of Zoology, Cytogenetics and Molecular Biology Lab., University of Kalyani, Kalyani, Nadia, 741235, India.,Department of Pharmaceutical Chemistry, Global Institute of Pharmaceutical Education and Research (Affiliated to Uttarakhand Technical University), Kashipur, 244713, India
| | - Asmita Samadder
- Department of Zoology, Cytogenetics and Molecular Biology Lab., University of Kalyani, Kalyani, Nadia, 741235, India
| | - Sisir Nandi
- Department of Pharmaceutical Chemistry, Global Institute of Pharmaceutical Education and Research (Affiliated to Uttarakhand Technical University), Kashipur, 244713, India
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33
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Yan X, Li Q, Jing L, Wu S, Duan W, Chen Y, Chen D, Pan X. Current advances on the phytochemical composition, pharmacologic effects, toxicology, and product development of Phyllanthi Fructus. Front Pharmacol 2022; 13:1017268. [PMID: 36339628 PMCID: PMC9626985 DOI: 10.3389/fphar.2022.1017268] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/30/2022] [Indexed: 12/01/2022] Open
Abstract
Phyllanthi Fructus (PF), the edible fruits of Phyllanthus emblica L., serves as an important resource for some health products, foods and drugs due to its high safety and sufficient nutritional value. In recent years, in vivo and in vitro experiments have been conducted to reveal the active components of PF. More than 180 compounds have been isolated and identified from the PF so far, primarily including tannins, phenolic acids, flavonoids, terpenoids, polysaccharides, fatty acids and amino acids. In traditional Chinese medicine (TCM), PF is used to cure several diseases such as bronchitis, asthma, diabetes, peptic ulcer, hepatopathy, leprosy, and jaundice. Consistent with ethnopharmacology, numerous modern studies have demonstrated that the extracts or monomeric compounds derived from PF exhibit various pharmacological effects including anti-oxidation, anti-bacteria, anti-inflammation, anti-tumour, anti-virus, immunity improvement, hypoglycemic and hypolipidemic effects, and multiple organ protective protection. Toxicological studies on PF indicated the absence of any adverse effects even at a high dose after oral administration. Due to strict quality control, these pharmacological activities and the safety of PF greatly improve the development and utilization of products. Our comprehensive review aims to summarize the phytochemistry, pharmacological effects, toxicology, and product development of PF to provide theoretical guidance and new insights for further research on PF in the future.
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Affiliation(s)
- Xiaoyu Yan
- School of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Qiuju Li
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Lin Jing
- School of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Shuangyue Wu
- School of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Wei Duan
- School of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yan Chen
- School of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Dayi Chen
- School of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- *Correspondence: Dayi Chen, ; Xiaoqi Pan,
| | - Xiaoqi Pan
- School of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- *Correspondence: Dayi Chen, ; Xiaoqi Pan,
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34
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Pitsillou E, Liang JJ, Beh RC, Hung A, Karagiannis TC. Molecular dynamics simulations highlight the altered binding landscape at the spike-ACE2 interface between the Delta and Omicron variants compared to the SARS-CoV-2 original strain. Comput Biol Med 2022; 149:106035. [PMID: 36055162 PMCID: PMC9420038 DOI: 10.1016/j.compbiomed.2022.106035] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 08/15/2022] [Accepted: 08/20/2022] [Indexed: 11/21/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) B.1.1.529 variant (Omicron), represents a significant deviation in genetic makeup and function compared to previous variants. Following the BA.1 sublineage, the BA.2 and BA.3 Omicron subvariants became dominant, and currently the BA.4 and BA.5, which are quite distinct variants, have emerged. Using molecular dynamics simulations, we investigated the binding characteristics of the Delta and Omicron (BA.1) variants in comparison to wild-type (WT) at the interface of the spike protein receptor binding domain (RBD) and human angiotensin converting enzyme-2 (ACE2) ectodomain. The primary aim was to compare our molecular modelling systems with previously published observations, to determine the robustness of our approach for rapid prediction of emerging future variants. Delta and Omicron were found to bind to ACE2 with similar affinities (-39.4 and -43.3 kcal/mol, respectively) and stronger than WT (-33.5 kcal/mol). In line with previously published observations, the energy contributions of the non-mutated residues at the interface were largely retained between WT and the variants, with F456, F486, and Y489 having the strongest energy contributions to ACE2 binding. Further, residues N440K, Q498R, and N501Y were predicted to be energetically favourable in Omicron. In contrast to Omicron, which had the E484A and K417N mutations, intermolecular bonds were detected for the residue pairs E484:K31 and K417:D30 in WT and Delta, in accordance with previously published findings. Overall, our simplified molecular modelling approach represents a step towards predictive model systems for rapidly analysing arising variants of concern.
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Affiliation(s)
- Eleni Pitsillou
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia; School of Science, STEM College, RMIT University, VIC, 3001, Australia
| | - Julia J Liang
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia; School of Science, STEM College, RMIT University, VIC, 3001, Australia
| | - Raymond C Beh
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia; Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3052, Australia
| | - Andrew Hung
- School of Science, STEM College, RMIT University, VIC, 3001, Australia
| | - Tom C Karagiannis
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia; Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3052, Australia.
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Liu J, Zhang L, Gao J, Zhang B, Liu X, Yang N, Liu X, Liu X, Cheng Y. Discovery of genistein derivatives as potential SARS-CoV-2 main protease inhibitors by virtual screening, molecular dynamics simulations and ADMET analysis. Front Pharmacol 2022; 13:961154. [PMID: 36091808 PMCID: PMC9452787 DOI: 10.3389/fphar.2022.961154] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 08/03/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Due to the constant mutation of virus and the lack of specific therapeutic drugs, the coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) still poses a huge threat to the health of people, especially those with underlying diseases. Therefore, drug discovery against the SARS-CoV-2 remains of great significance. Methods: With the main protease of virus as the inhibitor target, 9,614 genistein derivatives were virtually screened by LeDock and AutoDock Vina, and the top 20 compounds with highest normalized scores were obtained. Molecular dynamics simulations were carried out for studying interactions between these 20 compounds and the target protein. The drug-like properties, activity, and ADMET of these compounds were also evaluated by DruLiTo software or online server. Results: Twenty compounds, including compound 11, were screened by normalized molecular docking, which could bind to the target through multiple non-bonding interactions. Molecular dynamics simulation results showed that compounds 2, 4, 5, 11, 13, 14, 17, and 18 had the best binding force with the target protein of SARS-CoV-2, and the absolute values of binding free energies all exceeded 50 kJ/mol. The drug-likeness properties indicated that a variety of compounds including compound 11 were worthy of further study. The results of bioactivity score prediction found that compounds 11 and 12 had high inhibitory activities against protease, which indicated that these two compounds had the potential to be further developed as COVID-19 inhibitors. Finally, compound 11 showed excellent predictive ADMET properties including high absorption and low toxicity. Conclusion: These in silico work results show that the preferred compound 11 (ZINC000111282222), which exhibited strong binding to SARS-CoV-2 main protease, acceptable drug-like properties, protease inhibitory activity and ADMET properties, has great promise for further research as a potential therapeutic agent against COVID-19.
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Affiliation(s)
- Jiawei Liu
- Center for Drug Innovation and Discovery, College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Ling Zhang
- School of Chemical Technology, Shijiazhuang University, Shijiazhuang, China
| | - Jian Gao
- College of Plant Protection, Southwest University, Chongqing, China
| | - Baochen Zhang
- Center for Drug Innovation and Discovery, College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Xiaoli Liu
- Center for Drug Innovation and Discovery, College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Ninghui Yang
- Center for Drug Innovation and Discovery, College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Xiaotong Liu
- Center for Drug Innovation and Discovery, College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Xifu Liu
- Center for Drug Innovation and Discovery, College of Life Science, Hebei Normal University, Shijiazhuang, China
- *Correspondence: Xifu Liu, ; Yu Cheng,
| | - Yu Cheng
- Center for Drug Innovation and Discovery, College of Life Science, Hebei Normal University, Shijiazhuang, China
- *Correspondence: Xifu Liu, ; Yu Cheng,
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Investigating the structure-activity relationship of marine polycyclic batzelladine alkaloids as promising inhibitors for SARS-CoV-2 main protease (Mpro). Comput Biol Med 2022; 147:105738. [PMID: 35777088 PMCID: PMC9212445 DOI: 10.1016/j.compbiomed.2022.105738] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/04/2022] [Accepted: 06/11/2022] [Indexed: 11/24/2022]
Abstract
Over a span of two years ago, since the emergence of the first case of the novel coronavirus (SARS-CoV-2) in China, the pandemic has crossed borders causing serious health emergencies, immense economic crisis and impacting the daily life worldwide. Despite the discovery of numerous forms of precautionary vaccines along with other recently approved orally available drugs, yet effective antiviral therapeutics are necessarily needed to hunt this virus and its variants. Historically, naturally occurring chemicals have always been considered the primary source of beneficial medications. Considering the SARS-CoV-2 main protease (Mpro) as the duplicate key element of the viral cycle and its main target, in this paper, an extensive virtual screening for a focused chemical library of 15 batzelladine marine alkaloids, was virtually examined against SARS-CoV-2 main protease (Mpro) using an integrated set of modern computational tools including molecular docking (MDock), molecule dynamic (MD) simulations and structure-activity relationships (SARs) as well. The molecular docking predictions had disclosed four promising compounds including batzelladines H–I (8–9) and batzelladines F-G (6–7), respectively according to their prominent ligand-protein energy scores and relevant binding affinities with the (Mpro) pocket residues. The best two chemical hits, batzelladines H–I (8–9) were further investigated thermodynamically though studying their MD simulations at 100 ns, where they showed excellent stability within the accommodated (Mpro) pocket. Moreover, SARs studies imply the crucial roles of the fused tricyclic guanidinic moieties, its degree of unsaturation, position of the N–OH functionality and the length of the side chain as a spacer linking between two active sites, which disclosed fundamental structural and pharmacophoric features for efficient protein-ligand interaction. Such interesting findings are greatly highlighting further in vitro/vivo examinations regarding those marine natural products (MNPs) and their synthetic equivalents as promising antivirals.
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Contractor D, Globisch C, Swaroop S, Jain A. Structural basis of Omicron immune evasion: A comparative computational study. Comput Biol Med 2022; 147:105758. [PMID: 35763933 PMCID: PMC9212419 DOI: 10.1016/j.compbiomed.2022.105758] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 06/10/2022] [Accepted: 06/18/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND The vaccines used against SARS-CoV-2 by now have been able to develop some neutralising antibodies in the vaccinated population and their effectiveness has been challenged by the emergence of the new strains with numerous mutations in the spike protein of SARS-CoV-2. Since S protein is the major immunogenic protein of the virus which contains Receptor Binding Domain (RBD) that interacts with the human Angiotensin-Converting Enzyme 2 (ACE2) receptors, any mutations in this region should affect the neutralisation potential of the antibodies leading to the immune evasion. Several variants of concern of the virus have emerged so far, amongst which the most critical are Delta and recently reported Omicron. In this study, we have mapped and reported mutations on the modelled RBD and evaluated binding affinities of various human antibodies with it. METHOD Docking and molecular dynamics simulation studies have been used to explore the effect of mutations on the structure of RBD and RBD-antibody interaction. RESULTS These analyses show that the mutations mostly at the interface of a nearby region lower the binding affinity of the antibody by ten to forty percent, with a downfall in the number of interactions formed as a whole. It implies the generation of immune escape variants. CONCLUSIONS Notable mutations and their effect was characterised that explain the structural basis of antibody efficacy in Delta and a compromised neutralisation effect for the Omicron variant. Thus, our results pave the way for robust vaccine design that can be effective for many variants.
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Affiliation(s)
- Darshan Contractor
- Department of Bioengineering and Biotechnology, Birla Institute of Technology (BIT), Mesra, Ranchi, 835215, Jharkhand, India; Department of Biotechnology, Sun Pharmaceutical Industries Ltd., Tandalja, Vadodara, 390012, Gujarat, India
| | | | - Shiv Swaroop
- Department of Biochemistry, Central University of Rajasthan, NH-8, Bandar Sindri, Ajmer, 305817, Rajasthan, India.
| | - Alok Jain
- Department of Bioengineering and Biotechnology, Birla Institute of Technology (BIT), Mesra, Ranchi, 835215, Jharkhand, India.
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Mahaboob Ali AA, Bugarcic A, Naumovski N, Ghildyal R. Ayurvedic formulations: Potential COVID-19 therapeutics? PHYTOMEDICINE PLUS : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2022; 2:100286. [PMID: 35474908 PMCID: PMC9020642 DOI: 10.1016/j.phyplu.2022.100286] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2023]
Abstract
BACKGROUND While Molnupiravir and Paxlovid have recently been approved for use in some countries, there are no widely available treatments for COVID-19, the disease caused by SARS-CoV-2 infection. Herbal extracts have been used to treat respiratory clinical indications by Ayurvedic medicine practitioners with minimal adverse reactions and intense research efforts are currently under way to develop some of these formulations for COVID-19 treatment. METHODS Literature search for in silico, in vitro, in vivo, and clinical studies on the topic of Ayurvedic formulations for potential COVID-19 treatment, in order to present the current state of current knowledge by integrating information across all systems. RESULTS The search yielded 20 peer reviewed articles on in silico studies examining the interaction of phytoconstituents of popular Ayurvedic formulations with SARS-CoV-2 components and its receptors; five articles on preclinical investigations of the ability of selected Ayurvedic formulations to inhibit functions of SARS-CoV-2 proteins; and 51 completed clinical trials on the efficacy of using Ayurvedic formulations for treatment of mild to moderate COVID-19. Clinical data was available from 17 of the 51 trials. There was a considerable overlap between formulations used in the in silico studies and the clinical trials. This finding was unexpected as there is no clearly stated alignment between studies and the traditional pathway to drug discovery- basic discovery leading to in vitro and in vivo proof of concept, followed by validation in clinical trials. This was further demonstrated in the majority of the in silico studies where focus was on potential antiviral mechanisms, while the clinical trials were focused on patient recovery using oral treatments. In all 17 clinical trials where data was available, Ayurvedic treatments lead to a shorter period to recovery in participants with COVID-19. CONCLUSION The most commonly used Ayurvedic treatments for management of respiratory symptoms associated with SARS-CoV-2 infection appear to have prophylactic and/or therapeutic properties. It would be of particular interest to assess synergistic and concomitant systemic effects and antiviral activities of individual phytoconstituents and their combinations in the Ayurvedic treatments.
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Affiliation(s)
- Anees Ahmed Mahaboob Ali
- Centre for Research in Therapeutic Solutions, Faculty of Science and Technology, University of Canberra, Canberra, Australia
| | - Andrea Bugarcic
- National Centre for Naturopathic Medicine, Southern Cross University, Lismore, New South Wales, Australia
| | - Nenad Naumovski
- Functional Foods and Nutrition Research Laboratory, Faculty of Health, University of Canberra, Canberra, Ngunnawal Country, Australia
- Department of Nutrition-Dietetics, School of Health Science and Education, Harokopio University, Athens, Greece
| | - Reena Ghildyal
- Centre for Research in Therapeutic Solutions, Faculty of Science and Technology, University of Canberra, Canberra, Australia
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Xie J, Chen R, Wang Q, Mao H. Exploration and validation of Taraxacum mongolicum anti-cancer effect. Comput Biol Med 2022; 148:105819. [PMID: 35810695 DOI: 10.1016/j.compbiomed.2022.105819] [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: 04/01/2022] [Revised: 06/28/2022] [Accepted: 07/03/2022] [Indexed: 11/03/2022]
Abstract
Taraxacum mongolicum gained a lot of concern and was applied in 93 formulas in China due to its fame as a traditional Chinese medicine. The earliest recorded application of Taraxacum mongolicum was traced back to the Han dynasty. Generations of doctors boosted the usage and enriched the pharmacological mechanism. Clinical application of the Taraxacum mongolicum is flourishing as it treats multiple diseases. This study aims to explore the anti-cancer effect, retrieve the active ingredients and screen the key targets of Taraxacum mongolicum in cancer therapy. We collected and evaluated 10 key active compounds to investigate the anti-cancer effect via 69 significant targets and a variety of biological processes and pathways. Gene Ontology (GO) enrichment analysis uncovered targets associated with protein phosphorylation, cell proliferation and apoptotic processes via regulation of kinases, ATP and enzyme binding activities. Half of the top 20 enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were directly involved in cancer. Based on standard selection criteria, seven hub targets were obtained. These targets functioned through distinct patterns and pathways in realizing the anti-cancer effect. Molecular docking was conducted to validate the potential combination between compounds and hub targets to explore the pharmacological mechanism of key compounds in Taraxacum mongolicum against cancer. In summary, our findings indicate that the famous and widely used Chinese herb, Taraxacum mongolicum, shows good anti-cancer effect through its active compounds, targeted genes, and multiple involved biological processes. The results may provide a theoretical basis for subsequent experimental validation and drug development of Taraxacum mongolicum extract against cancer.
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Affiliation(s)
- Jumin Xie
- Hubei Key Laboratory of Renal Disease Occurrence and Intervention, Medical School, Hubei Polytechnic University, Huangshi, Hubei, 435003, PR China
| | - Ruxi Chen
- Hubei Key Laboratory of Renal Disease Occurrence and Intervention, Medical School, Hubei Polytechnic University, Huangshi, Hubei, 435003, PR China
| | - Qingzhi Wang
- Medical College of YiChun University, Xuefu Road No 576, Yichun, Jiangxi, 336000, PR China.
| | - Hui Mao
- Department of Dermatology, Huangshi Central Hospital, Huangshi, Hubei, 435000, PR China.
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Singh R, Bhardwaj VK, Das P, Bhattacherjee D, Zyryanov GV, Purohit R. Benchmarking the ability of novel compounds to inhibit SARS-CoV-2 main protease using steered molecular dynamics simulations. Comput Biol Med 2022; 146:105572. [PMID: 35551011 PMCID: PMC9052739 DOI: 10.1016/j.compbiomed.2022.105572] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 01/31/2023]
Abstract
BACKGROUND The SARS-CoV-2 main protease (Mpro) is an attractive target in the COVID-19 drug development process. It catalyzes the polyprotein's translation from viral RNA and specifies a particular cleavage site. Due to the absence of identical cleavage specificity in human cell proteases, targeting Mpro with chemical compounds can obstruct the replication of the virus. METHODS To explore the potential binding mechanisms of 1,2,3-triazole scaffolds in comparison to co-crystallized inhibitors 11a and 11b towards Mpro, we herein utilized molecular dynamics and enhanced sampling simulation studies. RESULTS AND CONCLUSION All the 1,2,3-triazole scaffolds interacted with catalytic residues (Cys145 and His41) and binding pocket residues of Mpro involving Met165, Glu166, Ser144, Gln189, His163, and Met49. Furthermore, the adequate binding free energy and potential mean force of the topmost compound 3h was comparable to the experimental inhibitors 11a and 11b of Mpro. Overall, the current analysis could be beneficial in developing the SARS-CoV-2 Mpro potential inhibitors.
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Affiliation(s)
- Rahul Singh
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP, 176061, India,Biotechnology Division, CSIR-IHBT, Palampur, HP, 176061, India,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Vijay Kumar Bhardwaj
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP, 176061, India,Biotechnology Division, CSIR-IHBT, Palampur, HP, 176061, India,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Pralay Das
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India,Natural Product Chemistry and Process Development, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Dhananjay Bhattacherjee
- Ural Federal University Named After the First President of Russia B. N. Yeltsin, 19 ul. Mira, 620002, Ekaterinburg, Russian Federation
| | - Grigory V. Zyryanov
- Ural Federal University Named After the First President of Russia B. N. Yeltsin, 19 ul. Mira, 620002, Ekaterinburg, Russian Federation,I. Ya. Postovsky Institute of Organic Synthesis, Ural Branch of the Russian Academy of Sciences, 22 ul. S. Kovalevskoi, 620219, Ekaterinburg, Russian Federation
| | - Rituraj Purohit
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP, 176061, India,Biotechnology Division, CSIR-IHBT, Palampur, HP, 176061, India,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India,Corresponding author. Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP, 176061, India
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Zahid S, Gul M, Shafique S, Rashid S. E2 UbcH5B-derived peptide ligands target HECT E3-E2 binding site and block the Ub-dependent SARS-CoV-2 egression: A computational study. Comput Biol Med 2022; 146:105660. [PMID: 35751189 PMCID: PMC9124161 DOI: 10.1016/j.compbiomed.2022.105660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 05/15/2022] [Accepted: 05/18/2022] [Indexed: 01/12/2023]
Abstract
Homologous to E6AP carboxyl-terminus (HECT)-type E3 ligase performs ubiquitin (Ub)-proteasomal protein degradation via forming a complex with E2∼Ub. Enveloped viruses including SARS-CoV-2 escape from the infected cells by harnessing the E-class vacuolar protein-sorting (ESCRT) machinery and mimic the cellular system through PPAY motif-based linking to HECT Ub ligase activity. In the present study, we have characterized the binding pattern of E2UbcH5B to HECT domains of NEDD4L, WWP1, WWP2, HECW1, and HECW2 through in silico analysis to isolate the E2UbcH5B-specific peptide inhibitors that may target SARS-CoV-2 viral egression. Molecular dynamics analysis revealed more opening of E2UbcH5B-binding pocket upon binding to HECTNEDD4L, HECTWWP1, HECTWWP2, HECTHECW1, and HECTHECW2. We observed similar binding pattern for E2UbcH5B and mentioned HECT domains as previously reported for HECTNEDD4L where Trp762, Trp709, and Trp657 residues of HECTNEDD4L, HECTWWP1, and HECTWWP2 are involved in making contacts with Ser94 residue of E2UbcH5B. Similarly, corresponding to HECTNEDD4L Tyr756 residue, HECTWWP1, HECTWWP2, HECTHECW1, and HECTHECW2-specific Phe703, Phe651, Phe1387, and Phe1353 residues execute interaction with E2UbcH5B. Our analysis suggests that corresponding to Cys942 of HECTNEDD4L, Cys890, Cys838, Cys1574, and Cys1540 residues of HECTWWP1, HECTWWP2, HECTHECW1, and HECTHECW2, respectively are involved in E2-to-E3 Ub transfer. Furthermore, MM-PBSA free energy calculations revealed favorable energy values for E2UbcH5B-HECT complexes along with the individual residue contributions. Subsequently, two E2UbcH5B-derived peptides (His55-Phe69 and Asn81-Ala96) were tested for their binding abilities against HECT domains of NEDD4L, WWP1, WWP2, HECW1, and HECW2. Their binding was validated through substitution of Phe62, Pro65, Ile84, and Cys85 residues into Ala, which revealed an impaired binding, suggesting that the proposed peptide ligands may selectively target E2-HECT binding and Ub-transfer. Collectively, we propose that peptide-driven blocking of E2-to-HECT Ub loading may limit SARS-CoV-2 egression and spread in the host cells.
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Kanchibhotla D, Subramanian S, Ravi Kumar RM, Venkatesh Hari KR, Pathania M. An In-vitro evaluation of a polyherbal formulation, against SARS-Cov-2. J Ayurveda Integr Med 2022; 13:100581. [PMID: 35753154 PMCID: PMC9222090 DOI: 10.1016/j.jaim.2022.100581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 02/19/2022] [Accepted: 04/16/2022] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND In the last two years, COVID-19 pandemic caused by SARS-CoV-2 has created a mass destruction among humanity causing a major health crisis around the world. With the emergence of new strains of the virus, lack of targeted drugs and antimicrobial resistance, there is a dire need to discover specific antiviral with minimum side effects targeted against COVID-19. OBJECTIVE The present study evaluates the antiviral efficacy of a novel Ayurvedic polyherbal formulation, NOQ19, composed of a 13 well known herbs, in a cell-based setting. METHODOLOGY Vero E6 (CL1008), the African green monkey kidney epithelial cell, were infected with SARS-CoV-2 virus (isolate USA-WA1/2020) in a 96 well-plate. NOQ19 test material was diluted at different concentration: 0.05 mg/ml, 0.1 mg/ml, 0.2 mg/ml, 0.3 mg/ml, 0.4 mg/ml, 0.5 mg/ml, 0.6 mg/ml, 0.7 mg/ml, 0.8 mg/ml and 0.9 mg/ml. These different concentrations of NOQ19 were added to infected cells respectively and incubated for 3 days in 5% CO2 incubator. Remdesivir was used as a positive control. The cells were finally fixed with formaldehyde, stained with crystal violet and plaques were visualized. The number of plaques were counted to determine the PFU(plaque forming units)/ml. RESULTS The results of the present study demonstrated an excellent an antiviral efficacy of NOQ19 at 0.9 mg/ml concentration, eliminating 100% virus. The IC50 of the drug was found to be 0.2 mg/ml. CONCLUSION There is limited data around pre-clinical efficacy of polyherbal Ayurvedic drugs. Ayurvedic and herbal formations need to be tested in a preclinical setting to support the human data. The results of the present study demonstrated viral load reduction using NOQ19 in Vero E6 cell lines infected with SARS-CoV-2 virus. These result along with other preclinical and clinical trials could further evaluate the efficacy of NOQ19 as a potential therapeutic option in the fighting the COVID-19 challenge.
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Xiang C, Chen C, Li X, Wu Y, Xu Q, Wen L, Xiong W, Liu Y, Zhang T, Dou C, Ding X, Hu L, Chen F, Yan Z, Liang L, Wei G. Computational approach to decode the mechanism of curcuminoids against neuropathic pain. Comput Biol Med 2022; 147:105739. [PMID: 35763932 DOI: 10.1016/j.compbiomed.2022.105739] [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: 03/11/2022] [Revised: 06/09/2022] [Accepted: 06/11/2022] [Indexed: 11/19/2022]
Abstract
BACKGROUND Curcumin (CUR), demethoxycurcumin (DMC) and bisdemethoxycurcumin (BDMC) are the main components of turmeric that commonly used to treat neuropathic pain (NP). However, the mechanism of the therapy is not sufficiently clarified. Herein, network pharmacology, molecular docking and molecular dynamics (MD) approaches were used to investigate the mechanism of curcuminoids for NP treatment. METHODS Active targets of curcuminoids were obtained from the Swiss Target database, and NP-related targets were retrieved from GeneCards, OMIM, Drugbank and TTD databases. A protein-protein interaction (PPI) network was built to screen the core targets. Furthermore, DAVID was used for GO and KEGG pathway enrichment analyses. Interactions between potential targets and curcuminoids were assessed by molecular docking and the MD simulations were run for 100ns to validate the docking results on the top six complexes. RESULTS CUR, DMC, and BDMC had 100, 99 and 100 targets respectively. After overlapping with NP there were 33, 33 and 31 targets respectively. PPI network analysis of TOP 10 core targets, TNF, GSK3β were common targets of curcuminoids. Molecular docking and MD results indicated that curcuminoids bind strongly with the core targets. The GO and KEGG showed that curcuminoids regulated nitrogen metabolism, the serotonergic synapse and ErbB signaling pathway to alleviate NP. Furthermore, specific targets in these three compounds were also analysed at the same time. CONCLUSIONS This study systematically explored and compared the anti-NP mechanism of curcuminoids, providing a novel perspective for their utilization.
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Affiliation(s)
- Chunxiao Xiang
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, China.
| | - Chunlan Chen
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, China.
| | - Xi Li
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, China.
| | - Yating Wu
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, China.
| | - Qing Xu
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, China.
| | - Lingmiao Wen
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, China.
| | - Wei Xiong
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, China.
| | - Yanjun Liu
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, China.
| | - Tinglan Zhang
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, China.
| | - Chongyang Dou
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, China.
| | - Xian Ding
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, China.
| | - Lin Hu
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, China.
| | - Fangfang Chen
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, China.
| | - Zhiyong Yan
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, China.
| | - Lingli Liang
- Department of Physiology and Pathophysiology, Institute of Neuroscience, Translational Medicine Institute, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shanxi, China.
| | - Guihua Wei
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, China.
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Alici H, Tahtaci H, Demir K. Design and various in silico studies of the novel curcumin derivatives as potential candidates against COVID-19 -associated main enzymes. Comput Biol Chem 2022; 98:107657. [PMID: 35259661 PMCID: PMC8881819 DOI: 10.1016/j.compbiolchem.2022.107657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 02/04/2022] [Accepted: 02/25/2022] [Indexed: 01/18/2023]
Abstract
The novel coronavirus disease (COVID-19) is a highly contagious disease caused by the SARS-CoV-2 virus, leading severe acute respiratory syndrome in patients. Although various antiviral drugs and their combinations have been tried so far against SARS-CoV-2 and they have shown some effectiveness, there is still a need for safe and cost-effective binding inhibitors in the fight against COVID-19. Therefore, phytochemicals in nature can be a quick solution due to their wide therapeutic spectrum and strong antiviral, anti-inflammatory, and antioxidant properties. In this context, the low toxicity, and high pharmacokinetic properties of curcumin, which is a natural phytochemical, as well as the easy synthesizing of its derivatives reveal the need for investigation of its various derivatives as inhibitors against coronaviruses. The present study focused on curcumin derivatives with reliable ADME profile and high molecular binding potency to different SARS-CoV-2 target enzymes (3CLPro, PLpro, NSP7/8/12, NSP7/8/12 +RNA, NSP15, NSP16, Spike, Spike+ACE). In the molecular docking studies, the best binding scores for the 22 proposed curcumin derivatives were obtained for the PLpro protein. Furthermore, MD simulations were performed for high-affinity ligand-PLpro protein complexes and subsequently, Lys157, Glu161, Asp164, Arg166, Glu167, Met208, Pro247, Pro248, Tyr264, Tyr273 and Asp302 residues of PLpro was determined to play key role for ligand binding by Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) analysis. The results of the study promise that the proposed curcumin derivatives can be potent inhibitors against SARS-CoV-2 and be converted into pharmaceutical drugs. It is also expected that the findings may provide guiding insights to future design studies for synthesizing different antiviral derivatives of phytochemicals.
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Affiliation(s)
- Hakan Alici
- Department of Physics, Faculty of Arts and Sciences, Zonguldak Bulent Ecevit University, 67100 Zonguldak, Turkey.
| | - Hakan Tahtaci
- Department of Chemistry, Faculty of Science, Karabuk University, 78050 Karabuk, Turkey
| | - Kadir Demir
- Department of Physics, Faculty of Arts and Sciences, Zonguldak Bulent Ecevit University, 67100 Zonguldak, Turkey
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Dwivedi M, Mukhopadhyay S, Yadav S, Dubey KD. A multidrug efflux protein in Mycobacterium tuberculosis; tap as a potential drug target for drug repurposing. Comput Biol Med 2022; 146:105607. [PMID: 35617724 DOI: 10.1016/j.compbiomed.2022.105607] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 05/02/2022] [Accepted: 05/09/2022] [Indexed: 11/27/2022]
Abstract
Tuberculosis (TB) is a serious communicative disease caused by Mycobacterium tuberculosis. Although there are vaccines and drugs available to treat the disease, they are not efficient, moreover, multidrug-resistant TB (MDR-TB) become a major hurdle in its therapy. These MDR strains utilize the multidrug efflux pump as a decisive weapon to fight against antitubercular drugs. Tap membrane protein was observed as a crucial multidrug efflux pump in M. tuberculosis and its critical implication in MDR-MTB development makes it an effective drug target. In the present study, we have utilized various in silico approaches to predict the applicability of FDA-approved ion channel inhibitors and blockers as therapeutic leads against Tuberculosis by targeting multidrug efflux protein; Tap in MTB. Tap protein structure is predicted by Phyre2 server followed by model refinement, validation, physio-chemical catheterization and target prediction. Further, the interaction between Tap protein and ligands were analysed by molecular docking and MD simulation run of 100 ns. Based on implication and compatibility, 18 FDA-approved ion channel inhibitors and blockers are selected as a ligand against the Tap protein and eventually observed five ligands; Glimepiride, Flecainide, Flupiritine, Nimodipine and Amlodipine as promising compounds which have exhibited the significant stable interaction with Tap protein and are proposed to modulate or interfere with its activity. These compounds illustrated the substantial docking score and total binding enthalpy more than -7 kcal/mol and -42 kcal/mol respectively which implies that the selected FDA-approved compounds can spontaneously interact with the Tap protein to modulate its function. This study proposed Tap protein as a prominent drug target in MTB and investigated compounds that show considerable interaction with the Tap protein as potential therapeutic molecules. These interactions may lead to modulating or inhibit the activity of drug efflux protein thereby making MTB susceptible to antitubercular drugs.
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Affiliation(s)
- Manish Dwivedi
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, 226028, India.
| | - Sutanu Mukhopadhyay
- Department of Chemistry, Ramakrishna Mission Vivekananda Centenary College, West Bengal, India
| | - Shalini Yadav
- Department of Chemistry, Shiv Nadar University, Greater Noida, 201314, India
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46
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Antiviral phytocompounds “ellagic acid” and “(+)-sesamin” of Bridelia retusa identified as potential inhibitors of SARS-CoV-2 3CL pro using extensive molecular docking, molecular dynamics simulation studies, binding free energy calculations, and bioactivity prediction. Struct Chem 2022; 33:1445-1465. [PMID: 35571865 PMCID: PMC9086128 DOI: 10.1007/s11224-022-01959-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 04/28/2022] [Indexed: 12/24/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected billions and has killed millions to date. Studies are being carried out to find therapeutic molecules that can potentially inhibit the replication of SARS-CoV-2. 3-chymotrypsin-like protease (3CL pro) involved in the polyprotein cleavage process is believed to be the key target for viral replication, and hence is an attractive target for the discovery of antiviral molecules. In the present study, we aimed to identify natural phytocompounds from Bridelia retusa as potential inhibitors of SARS-CoV-2 3CL pro (PDB ID: 6M2N) using in silico techniques. Molecular docking studies conducted with three different tools in triplicates revealed that ellagic acid (BR6) and (+)-sesamin (BR13) has better binding affinity than the co-crystal inhibitor “3WL” of 6M2N. BR6 and BR13 were found to have a high LD50 value with good bioavailability. 3WL, BR6, and BR13 bind to the same active binding site and interacted with the HIS41-CYS145 catalytic dyad including other crucial amino acids. Molecular dynamics simulation studies revealed stability of protein–ligand complexes as evidenced from root-mean-square deviations, root-mean-square fluctuations (RMSF), protein secondary structure elements, ligand-RMSF, protein–ligand contacts, ligand torsions, and ligand properties. BR6 (−22.3064 kcal/mol) and BR13 (−19.1274 kcal/mol) showed a low binding free energy value. The Bayesian statistical model revealed BR6 and BR13 as better protease inhibitors than 3WL. Moreover, BR6 and BR13 had already been reported to elicit antiviral activities. Therefore, we conclude that ellagic acid and (+)-sesamin as natural antiviral phytocompounds with inhibitory potential against SARS-CoV-2 3CL pro.
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Yousaf R, Navid A, Azam SS. Discovery of novel Glutaminase allosteric inhibitors through drug repurposing and comparative MMGB/PBSA and molecular dynamics simulation. Comput Biol Med 2022; 146:105669. [PMID: 35654625 DOI: 10.1016/j.compbiomed.2022.105669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 05/21/2022] [Accepted: 05/23/2022] [Indexed: 11/03/2022]
Abstract
GLS1 enzymes (Glutaminase C (GAC) and kidney-type Glutaminase (KGA)) are gaining prominence as a target for tumor treatment including lung, breast, kidney, prostate, and colorectal. To date, several medicinal chemistry studies are being conducted to develop new and effective inhibitors against GLS1 enzymes. Telaglenastat, a drug that targets the allosteric site of GLS1, has undergone clinical trials for the first time for the therapy of solid tumors and hematological malignancies. A comprehensive computational investigation is performed to get insights into the inhibition mechanism of the Telaglenastat. Some novel inhibitors are also proposed against GLS1 enzymes using the drug repurposing approach using 2D-fingerprinting virtual screening method against 2.4 million compounds, application of pharmacokinetics, Molecular Docking, and Molecular Dynamic (MD) Simulations. A TIP3P water box of 10 Å was defined to solvate both enzymes to improve MD simulation reliability. The dynamics results were validated further by the MMGB/PBSA binding free energy method, RDF, and AFD analysis. Results of these computational analysis revealed a stable binding affinity of Telaglenastat, as well as an FDA approved drug Astemizole (IC50 ∼ 0.9 nM) and a novel para position oriented methoxy group containing Chembridge compound (Chem-64284604) that provides an effective inhibitory action against GAC and KGA.
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Prasetyo WE, Purnomo H, Sadrini M, Wibowo FR, Firdaus M, Kusumaningsih T. Identification of potential bioactive natural compounds from Indonesian medicinal plants against 3-chymotrypsin-like protease (3CL pro) of SARS-CoV-2: molecular docking, ADME/T, molecular dynamic simulations, and DFT analysis. J Biomol Struct Dyn 2022:1-18. [DOI: 10.1080/07391102.2022.2068071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Wahyu Eko Prasetyo
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Sebelas Maret University, Surakarta, Indonesia
| | - Heri Purnomo
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Sebelas Maret University, Surakarta, Indonesia
| | - Miracle Sadrini
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Sebelas Maret University, Surakarta, Indonesia
| | - Fajar Rakhman Wibowo
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Sebelas Maret University, Surakarta, Indonesia
| | - Maulidan Firdaus
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Sebelas Maret University, Surakarta, Indonesia
| | - Triana Kusumaningsih
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Sebelas Maret University, Surakarta, Indonesia
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Reckoning apigenin and kaempferol as a potential multi-targeted inhibitor of EGFR/HER2-MEK pathway of metastatic colorectal cancer identified using rigorous computational workflow. Mol Divers 2022; 26:3337-3356. [PMID: 35147860 DOI: 10.1007/s11030-022-10396-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 01/22/2022] [Indexed: 11/27/2022]
Abstract
In the past two decades, the treatment of metastatic colorectal cancer (mCRC) has been revolutionized as multiple cytotoxic, biological, and targeted drugs are being approved. Unfortunately, tumors treated with single targeted agents or therapeutics usually develop resistance. According to pathway-oriented screens, mCRC cells evade EGFR inhibition by HER2 amplification and/or activating Kras-MEK downstream signaling. Therefore, treating mCRC patients with dual EGFR/HER2 inhibitors, MEK inhibitors, or the combination of the two drugs envisaged to prevent the resistance development which eventually improves the overall survival rate. In the present study, we aimed to screen potential phytochemical lead compounds that could multi-target EGFR, HER2, and MEK1 (Mitogen-activated protein kinase kinase) using a computer-aided drug design approach that includes molecular docking, endpoint binding free energy calculation using MM-GBSA, ADMET, and molecular dynamics (MD) simulations. Docking studies revealed that, unlike all other ligands, apigenin and kaempferol exhibit the highest docking score against all three targets. Details of ADMET analysis, MM/GBSA, and MD simulations helped us to conclusively determine apigenin and kaempferol as potentially an inhibitor of EGFR, HER2, and MEK1 apigenin and kaempferol against mCRC at a systemic level. Additionally, both apigenin and kaempferol elicited antiangiogenic properties in a dose-dependent manner. Collectively, these findings provide the rationale for drug development aimed at preventing CRC rather than intercepting resistance.
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Prathiviraj R, Chellapandi P, Begum A, Kiran GS, Selvin J. Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. Virus Res 2022; 307:198618. [PMID: 34740719 PMCID: PMC8563081 DOI: 10.1016/j.virusres.2021.198618] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 01/01/2023]
Abstract
The second wave of COVID-19 caused by severe acute respiratory syndrome virus (SARS-CoV-2) is rapidly spreading over the world. Mechanisms behind the flee from current antivirals are still unclear due to the continuous occurrence of SARS-CoV-2 genetic variants. Brazil is the world's second-most COVID-19 affected country. In the present study, we identified the genomic and proteomic variants of Brazilian SARS-CoV-2 isolates. We identified 16 different genotypic variants were found among the 27 isolates. The genotypes of three isolates such as Bra/1236/2021 (G15), Bra/MASP2C844R2/2020 (G11), and Bra/RJ-DCVN5/2020 (G9) have a unique mutant in NSP4 (S184N), 2'O-Mutase (R216N), membrane protein (A2V) and Envelope protein (V5A). A mutation in RdRp of SARS-CoV-2, particularly the change of Pro-to Leu-at 323 resulted in the stabilization of the structure in BRA/CD1739-P4/2020. NSP4, NSP5 protein mutants are more virulent in genotype 15 and 16. A fast protein folding rate changes the structural stability and leads to escape for current antivirals. Thus, our findings help researchers to develop the best potent antivirals based on the new mutant of Brazilian isolates.
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Affiliation(s)
| | - Paulchamy Chellapandi
- Department of Bioinformatics, Bharathidasan University, Tiruchirappalli 620024, India
| | - Ajima Begum
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - George Seghal Kiran
- Department of Food Science and Technology, Pondicherry University, Puducherry 605014, India
| | - Joseph Selvin
- Department of Microbiology, Pondicherry University, Puducherry 605014, India
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