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Bailly C. Covalent binding of withanolides to cysteines of protein targets. Biochem Pharmacol 2024; 226:116405. [PMID: 38969301 DOI: 10.1016/j.bcp.2024.116405] [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: 03/29/2024] [Revised: 05/26/2024] [Accepted: 07/01/2024] [Indexed: 07/07/2024]
Abstract
Withanolides represent an important category of natural products with a steroidal lactone core. Many of them contain an α,β-unsaturated carbonyl moiety with a high reactivity toward sulfhydryl groups, including protein cysteine thiols. Different withanolides endowed with marked antitumor and anti-inflammatory have been shown to form stable covalent complexes with exposed cysteines present in the active site of oncogenic kinases (BTK, IKKβ, Zap70), metabolism enzymes (Prdx-1/6, Pin1, PHGDH), transcription factors (Nrf2, NFκB, C/EBPβ) and other structural and signaling molecules (GFAP, β-tubulin, p97, Hsp90, vimentin, Mpro, IPO5, NEMO, …). The present review analyzed the covalent complexes formed through Michael addition alkylation reactions between six major withanolides (withaferin A, physalin A, withangulatin A, 4β-hydroxywithanolide E, withanone and tubocapsanolide A) and key cysteine residues of about 20 proteins and the resulting biological effects. The covalent conjugation of the α,β-unsaturated carbonyl system of withanolides with reactive protein thiols can occur with a large set of soluble and membrane proteins. It points to a general mechanism, well described with the leading natural product withaferin A, but likely valid for most withanolides harboring a reactive (electrophilic) enone moiety susceptible to react covalently with cysteinyl residues of proteins. The multiplicity of reactive proteins should be taken into account when studying the mechanism of action of new withanolides. Proteomic and network analyses shall be implemented to capture and compare the cysteine covalent-binding map for the major withanolides, so as to identify the protein targets at the origin of their activity and/or unwanted effects. Screening of the cysteinome will help understanding the mechanism of action and designing cysteine-reactive electrophilic drug candidates.
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Affiliation(s)
- Christian Bailly
- CNRS, Inserm, CHU Lille, UMR9020-U1277-CANTHER-Cancer Heterogeneity Plasticity and Resistance to Therapies, OncoLille Institute, University of Lille, F-59000 Lille, France; Institute of Pharmaceutical Chemistry Albert Lespagnol (ICPAL), Faculty of Pharmacy, University of Lille, F-59006 Lille, France; OncoWitan, Scientific Consulting Office, F-59290 Lille, France.
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Kumar V, Meidinna HN, Kaul SC, Gupta D, Ishida Y, Terao K, Vrati S, Sundar D, Wadhwa R. Molecular insights to the anti-COVID-19 potential of α-, β- and γ-cyclodextrins. J Biomol Struct Dyn 2023:1-11. [PMID: 38116950 DOI: 10.1080/07391102.2023.2294385] [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: 08/10/2023] [Accepted: 12/05/2023] [Indexed: 12/21/2023]
Abstract
SARS-CoV-2 viral infection is regulated by the host cell receptors ACE2 and TMPRSS2, and therefore the effect of various natural and synthetic compounds on these receptors has recently been the subject of investigations. Cyclodextrins, naturally occurring polysaccharides derived from starch, are soluble in water and have a hydrophobic cavity at their center enabling them to accommodate small molecules and utilize them as carriers in the food, supplements, and pharmaceutical industries to improve the solubility, stability, and bioavailability of target compounds. In the current study, computational molecular simulations were used to investigate the ability of α-, β- and γ-Cyclodextrins on human cell surface receptors. Cell-based experimental approaches, including expression analyses at mRNA and protein levels and virus replication, were used to assess the effect on receptor expression and virus infection, respectively. We found that none of the three CDs could dock effectively to human cell surface receptor ACE2 and viral protease Mpro (essential for virus replication). On the other hand, α- and β-CD showed strong and stable interactions with TMPRSS2, and the expression of both ACE2 and TMPRSS2 was downregulated at the mRNA and protein levels in cyclodextrin (CD)-treated cells. A cell-based virus replication assay showed ∼20% inhibition by β- and γ-CD. Taken together, the study suggested that (i) downregulation of expression of host cell receptors may not be sufficient to inhibit virus infection (ii) activity of the receptors and virus protein Mpro may play a critical and clinically relevant role, and hence (iii) newly emerging anti-Covid-19 compounds warrant multimodal functional analyses.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Vipul Kumar
- DAILAB, Department of Biochemical Engineering & Biotechnology, Indian Institute of Technology (IIT) Delhi, Hauz Khas, New Delhi, India
| | - Hazna Noor Meidinna
- AIST-INDIA DAILAB, National Institute of Advanced Industrial Science & Technology (AIST), Tsukuba, Japan
| | - Sunil C Kaul
- AIST-INDIA DAILAB, National Institute of Advanced Industrial Science & Technology (AIST), Tsukuba, Japan
| | | | | | - Keiji Terao
- CycloChem Bio Co., Ltd, Chuo-ku, Kobe, Japan
| | | | - Durai Sundar
- DAILAB, Department of Biochemical Engineering & Biotechnology, Indian Institute of Technology (IIT) Delhi, Hauz Khas, New Delhi, India
| | - Renu Wadhwa
- AIST-INDIA DAILAB, National Institute of Advanced Industrial Science & Technology (AIST), Tsukuba, Japan
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3
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Xing Z, Su A, Mi L, Zhang Y, He T, Qiu Y, Wei T, Li Z, Zhu J, Wu W. Withaferin A: A Dietary Supplement with Promising Potential as an Anti-Tumor Therapeutic for Cancer Treatment - Pharmacology and Mechanisms. Drug Des Devel Ther 2023; 17:2909-2929. [PMID: 37753228 PMCID: PMC10519218 DOI: 10.2147/dddt.s422512] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 08/18/2023] [Indexed: 09/28/2023] Open
Abstract
Cancer, as the leading cause of death worldwide, poses a serious threat to human health, making the development of effective tumor treatments a significant challenge. Natural products continue to serve as crucial resources for drug discovery. Among them, Withaferin A (WA), the most active phytocompound extracted from the renowned dietary supplement Withania somnifera (L.) Dunal, exhibits remarkable anti-tumor efficacy. In this manuscript, we aim to comprehensively summarize the pharmacological characteristics of WA as a potential anti-tumor drug candidate, with the objective of contributing to its further development and the discovery of prospective drugs. Through an extensive review of literature from PubMed, Science Direct, and Web of Science, we have gathered substantial evidence showcasing WA's significant anti-tumor effects against a wide range of cancers in both in vitro and in vivo studies. Mechanistically, WA exerts its anti-tumor influence by inducing cell cycle arrest, apoptosis, autophagy, and ferroptosis. Additionally, it inhibits cell proliferation, cancer stem cells, tumor metastasis, and also suppresses epithelial-mesenchymal transition (EMT) and angiogenesis. Several studies have identified direct target proteins of WA, such as vimentin, Hsp90, annexin II and mFAM72A, while BCR-ABL, Mortalin (mtHsp70), Nrf2, and c-MYB are potential targets of WA. Notwithstanding its remarkable anti-tumor efficacy, there are some limitations associated with WA, including potential toxicity and poor oral bioavailability, which need to be addressed when considering it as an anti-tumor candidate agent. Nevertheless, I given its promising anti-tumor attributes, WA remains an encouraging candidate for future drug development. Unveiling the exact target and comprehensive mechanism of WA's action represents a crucial research direction to pursue in the future.
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Affiliation(s)
- Zhichao Xing
- Division of Thyroid Surgery, Department of General Surgery and Laboratory of Thyroid and Parathyroid Disease, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, People’s Republic of China
| | - Anping Su
- Division of Thyroid Surgery, Department of General Surgery and Laboratory of Thyroid and Parathyroid Disease, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, People’s Republic of China
| | - Li Mi
- Division of Thyroid Surgery, Department of General Surgery and Laboratory of Thyroid and Parathyroid Disease, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, People’s Republic of China
| | - Yujie Zhang
- Division of Thyroid Surgery, Department of General Surgery and Laboratory of Thyroid and Parathyroid Disease, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, People’s Republic of China
| | - Ting He
- Division of Thyroid Surgery, Department of General Surgery and Laboratory of Thyroid and Parathyroid Disease, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, People’s Republic of China
| | - Yuxuan Qiu
- Department of Ultrasound, West China Hospital, Sichuan University, Chengdu, People’s Republic of China
| | - Tao Wei
- Division of Thyroid Surgery, Department of General Surgery and Laboratory of Thyroid and Parathyroid Disease, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, People’s Republic of China
| | - Zhihui Li
- Division of Thyroid Surgery, Department of General Surgery and Laboratory of Thyroid and Parathyroid Disease, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, People’s Republic of China
| | - Jingqiang Zhu
- Division of Thyroid Surgery, Department of General Surgery and Laboratory of Thyroid and Parathyroid Disease, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, People’s Republic of China
| | - Wenshuang Wu
- Division of Thyroid Surgery, Department of General Surgery and Laboratory of Thyroid and Parathyroid Disease, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, People’s Republic of China
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Kumar V, Sari AN, Meidinna HN, Kaul A, Basu B, Ishida Y, Terao K, Kaul SC, Vrati S, Sundar D, Wadhwa R. Computational and experimental evidence of the anti-COVID-19 potential of honeybee propolis ingredients, caffeic acid phenethyl ester and artepillin c. Phytother Res 2023; 37:3651-3654. [PMID: 36757055 DOI: 10.1002/ptr.7717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 02/10/2023]
Affiliation(s)
- Vipul Kumar
- DAILAB, Department of Biochemical Engineering & Biotechnology, Indian Institute of Technology (IIT) Delhi, New Delhi, India
| | - Anissa Nofita Sari
- AIST-INDIA DAILAB, National Institute of Advanced Industrial Science & Technology (AIST), Tsukuba, Japan
- School of Integrative & Global Majors (SIGMA), University of Tsukuba, Tsukuba, Japan
| | - Hazna Noor Meidinna
- AIST-INDIA DAILAB, National Institute of Advanced Industrial Science & Technology (AIST), Tsukuba, Japan
- School of Integrative & Global Majors (SIGMA), University of Tsukuba, Tsukuba, Japan
| | - Ashish Kaul
- AIST-INDIA DAILAB, National Institute of Advanced Industrial Science & Technology (AIST), Tsukuba, Japan
- School of Integrative & Global Majors (SIGMA), University of Tsukuba, Tsukuba, Japan
| | - Brohmomoy Basu
- Regional Centre for Biotechnology (RCB), Faridabad, India
| | | | | | - Sunil C Kaul
- AIST-INDIA DAILAB, National Institute of Advanced Industrial Science & Technology (AIST), Tsukuba, Japan
| | | | - Durai Sundar
- DAILAB, Department of Biochemical Engineering & Biotechnology, Indian Institute of Technology (IIT) Delhi, New Delhi, India
| | - Renu Wadhwa
- AIST-INDIA DAILAB, National Institute of Advanced Industrial Science & Technology (AIST), Tsukuba, Japan
- School of Integrative & Global Majors (SIGMA), University of Tsukuba, Tsukuba, Japan
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Ramli S, Wu YS, Batumalaie K, Guad RM, Choy KW, Kumar A, Gopinath SCB, Rahman Sarker MM, Subramaniyan V, Sekar M, Fuloria NK, Fuloria S, Chinni SV, Ramachawolran G. Phytochemicals of Withania somnifera as a Future Promising Drug against SARS-CoV-2: Pharmacological Role, Molecular Mechanism, Molecular Docking Evaluation, and Efficient Delivery. Microorganisms 2023; 11:microorganisms11041000. [PMID: 37110423 PMCID: PMC10142625 DOI: 10.3390/microorganisms11041000] [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: 03/14/2023] [Revised: 04/02/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
Coronavirus disease (COVID-19) has killed millions of people since first reported in Wuhan, China, in December 2019. Intriguingly, Withania somnifera (WS) has shown promising antiviral effects against numerous viral infections, including SARS-CoV and SARS-CoV-2, which are contributed by its phytochemicals. This review focused on the updated testing of therapeutic efficacy and associated molecular mechanisms of WS extracts and their phytochemicals against SARS-CoV-2 infection in preclinical and clinical studies with the aim to develop a long-term solution against COVID-19. It also deciphered the current use of the in silico molecular docking approach in developing potential inhibitors from WS targeting SARS-CoV-2 and host cell receptors that may aid the development of targeted therapy against SARS-CoV-2 ranging from prior to viral entry until acute respiratory distress syndrome (ARDS). This review also discussed nanoformulations or nanocarriers in achieving effective WS delivery to enhance its bioavailability and therapeutic efficacy, consequently preventing the emergence of drug resistance, and eventually therapeutic failure.
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Affiliation(s)
- Suaidah Ramli
- Department of Pharmacy, Hospital Sultanah Nur Zahirah, Kuala Terengganu 20400, Malaysia
| | - Yuan Seng Wu
- Centre for Virus and Vaccine Research, School of Medical and Life Sciences, Sunway University, Subang Jaya 47500, Malaysia
- Department of Biological Sciences, School of Medical and Life Sciences, Sunway University, Subang Jaya 47500, Malaysia
| | - Kalaivani Batumalaie
- Department of Biomedical Sciences, Faculty of Health Sciences, Asia Metropolitan University, Johor Bahru 81750, Malaysia
| | - Rhanye Mac Guad
- Department of Biomedical Science and Therapeutics, Faculty of Medicine and Health Science, Universiti Malaysia Sabah, Kota Kinabalu 88400, Malaysia
| | - Ker Woon Choy
- Department of Anatomy, Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh 47000, Malaysia
| | - Ashok Kumar
- Department of Internal Medicine, Division of Pulmonary, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA
| | - Subash C B Gopinath
- Centre of Excellence (CoE), Faculty of Chemical Engineering & Technology & Micro System Technology, Universiti Malaysia Perlis (UniMAP), Arau 02600, Malaysia
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis (UniMAP), Kangar 01000, Malaysia
| | - Md Moklesur Rahman Sarker
- Department of Pharmacy, State University of Bangladesh, 77 Satmasjid Road, Dhanmondi, Dhaka 1205, Bangladesh
- Health Med Science Research Network, 3/1, Block F, Lalmatia, Dhaka 1207, Bangladesh
| | - Vetriselvan Subramaniyan
- Pharmacology Unit, Jeffrey Cheah School of Medicine and Health Sciences, MONASH University, Jalan Lagoon Selatan, Bandar Sunway, Subang Jaya 47500, Malaysia
- Department of Pharmacology, School of Medicine, Faculty of Medicine, Bioscience and Nursing, MAHSA University, Subang Jaya 42610, Malaysia
| | - Mahendran Sekar
- School of Pharmacy, Monash University Malaysia, Bandar Sunway, Subang Jaya 47500, Malaysia
| | - Neeraj Kumar Fuloria
- Centre of Excellence for Biomaterials Engineering & Faculty of Pharmacy, AIMST University, Bedong 08100, Malaysia
- Center for Transdisciplinary Research, Department of Pharmacology, Saveetha Institute of Medical and Technical Sciences, Saveetha Dental College and Hospitals, Saveetha University, Chennai 600077, India
| | - Shivkanya Fuloria
- Faculty of Pharmacy, AIMST University, Semeling, Bedong 08100, Malaysia
| | - Suresh V Chinni
- Department of Biochemistry, Faculty of Medicine, Bioscience, and Nursing, MAHSA University, Jenjarom 42610, Malaysia
- Department of Periodontics, Saveetha Institute of Medical and Technical Sciences, Saveetha Dental College and Hospitals, Chennai 600077, India
| | - Gobinath Ramachawolran
- Department of Foundation, RCSI & UCD Malaysia Campus, No 4, Jalan Sepoy Lines, Georgetown 10450, Malaysia
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Kashyap D, Jakhmola S, Tiwari D, Kumar R, Moorthy NSHN, Elangovan M, Brás NF, Jha HC. Plant derived active compounds as potential anti SARS-CoV-2 agents: an in-silico study. J Biomol Struct Dyn 2022; 40:10629-10650. [PMID: 34225565 DOI: 10.1080/07391102.2021.1947384] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Plants are a valued potential source of drugs for a variety of diseases and are often considered less toxic to humans. We investigated antiviral compounds that may potentially target SARS-CoV-2 antigenic spike (S) and host proteins; angiotensin-converting enzyme2 (ACE2), and transmembrane serine protease2 (TMPRSS2). We scrutinized 36 phytochemicals from 15 Indian medicinal plants known to be effective against RNA viruses via molecular docking. Besides, the TMPRSS2 structure was modeled and validated using the SWISS-MODEL. Docking was performed using Autodock Vina and 4.2 followed by visualization of the docking poses on Pymol version 2.4.0 and Discovery Studio Visualizer. Molecular docking showed that 12 out of 36 active compounds interacted efficiently with S, ACE2, and TMPRSS2 proteins. The ADMET profile generated using the swissADME and pkCSM server revealed that these compounds were possessed druggable properties. The Amber 12 simulation package was used to carry out energy minimizations and molecular dynamics (MD) simulations. The total simulation time for both S protein: WFA and S protein: WND complexes was 300 ns (100 ns per replica). A total of 120 structures were extracted from the last 60 ns of each MD simulation for further analysis. MM-PBSA and MM-GBSA were employed to assess the binding energy of each ligand and the receptor-binding domain of the viral S-protein. The methods suggested that WND and WFA showed thermodynamically favorable binding energies, and the S protein had a higher affinity with WND. Interestingly, Leu455 hotspot residue in the S protein, also predicted to participate in binding with ACE2, was engaged by WND and WFA. HighlightsPlants' natural active compounds may aid in the development of COVID-19 therapeutics.MD simulation study revealed stable binding of withanolide D and withaferin A with spike proteinWithanolide D and withaferin A could be effective against SARS-CoV-2 spike protein.Discovery of druggable agents that have less or lack of binding affinity with ACE2 to avoid the organs associated with comorbidities.According to ADMET selected phytochemicals may be used as druggable compounds.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dharmendra Kashyap
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Shweta Jakhmola
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Deeksha Tiwari
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Rajesh Kumar
- Department of Physics, Indian Institute of Technology Indore, Indore, India
| | | | | | - Natércia F Brás
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Hem Chandra Jha
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
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Gheshlaghi SZ, Nakhaei E, Ebrahimi A, Jafari M, Shahraki A, Rezazadeh S, Saberinasab E, Nowroozi A, Hosseini SS. Analysis of medicinal and therapeutic potential of Withania somnifera derivatives against COVID-19. J Biomol Struct Dyn 2022:1-11. [PMID: 35993530 DOI: 10.1080/07391102.2022.2112977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
Apart from chemical and allopathic drugs, several medicinal plants contain phytochemicals that are potentially useful to counter the COVID-19 pandemic. Withania somnifera (Ashwagandha), which has a good effect on some viral infections, can be considered as a candidate against the virus. In the present study, thirty-nine natural compounds of Ashwagandha were investigated in terms of their binding to the important drug targets to treat the COVID-19. Although the molecular docking calculations reveal the binding affinities of the compounds to Mpro, TMPRSS2, NSP15, PLpro, Spike RBD + ACE2, RdRp and NSP12 as targets in controlling the coronavirus enzymes, Withanoside II is expected to be the most effective compound due to the high affinity in binding with many of considered targets. Furthermore, the Withanoside III, IV, V, X, and XI have favorable binding affinities as ligands with respect to the MM/GBSA calculations. The molecular dynamics simulations MD explore a stable hydrogen bond network between ligands and the active sites residues. Also, the dynamic fluctuations of the binding site residues verify their tight binding to ligands. Moreover, the stability of ligand-protein complexes is approved by the RMSD ranges lower than 0.5 Å in equilibration zone for all mentioned complexes. The TMPRSS2-Withanolide Q and Mpro-Withanoside IV complexes are the most stable pairs using the MM/GBSA calculations and MD simulation.
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Affiliation(s)
- Saman Zare Gheshlaghi
- Department of Chemistry, Computational Quantum Chemistry Laboratory, University of Sistan and Baluchestan, Zahedan, Iran
| | - Ebrahim Nakhaei
- Department of Chemistry, Computational Quantum Chemistry Laboratory, University of Sistan and Baluchestan, Zahedan, Iran
| | - Ali Ebrahimi
- Department of Chemistry, Computational Quantum Chemistry Laboratory, University of Sistan and Baluchestan, Zahedan, Iran
| | - Majid Jafari
- Department of Plant Protection, Higher Education Complex of Saravan, College of Agriculture
| | - Asiyeh Shahraki
- Department of Chemistry, Computational Quantum Chemistry Laboratory, University of Sistan and Baluchestan, Zahedan, Iran
| | - Shiva Rezazadeh
- Department of Chemistry, Computational Quantum Chemistry Laboratory, University of Sistan and Baluchestan, Zahedan, Iran
| | - Erfan Saberinasab
- School of Health, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Alireza Nowroozi
- Department of Chemistry, Computational Quantum Chemistry Laboratory, University of Sistan and Baluchestan, Zahedan, Iran
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Rieder AS, Deniz BF, Netto CA, Wyse ATS. A Review of In Silico Research, SARS-CoV-2, and Neurodegeneration: Focus on Papain-Like Protease. Neurotox Res 2022; 40:1553-1569. [PMID: 35917086 PMCID: PMC9343570 DOI: 10.1007/s12640-022-00542-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/17/2022] [Accepted: 06/30/2022] [Indexed: 01/18/2023]
Abstract
Since the appearance of SARS-CoV-2 and the COVID-19 pandemic, the search for new approaches to treat this disease took place in the scientific community. The in silico approach has gained importance at this moment, once the methodologies used in this kind of study allow for the identification of specific protein–ligand interactions, which may serve as a filter step for molecules that can act as specific inhibitors. In addition, it is a low-cost and high-speed technology. Molecular docking has been widely used to find potential viral protein inhibitors for structural and non-structural proteins of the SARS-CoV-2, aiming to block the infection and the virus multiplication. The papain-like protease (PLpro) participates in the proteolytic processing of SARS-CoV-2 and composes one of the main targets studied for pharmacological intervention by in silico methodologies. Based on that, we performed a systematic review about PLpro inhibitors from the perspective of in silico research, including possible therapeutic molecules in relation to this viral protein. The neurological problems triggered by COVID-19 were also briefly discussed, especially relative to the similarities of neuroinflammation present in Alzheimer’s disease. In this context, we focused on two molecules, curcumin and glycyrrhizinic acid, given their PLpro inhibitory actions and neuroprotective properties and potential therapeutic effects on COVID-19.
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Affiliation(s)
- Alessandra S Rieder
- Laboratory of Neuroprotection and Neurometabolic Diseases, Wyse's Lab, Department of Biochemistry, ICBS, Universidade Federal Do Rio Grande Do Sul (UFRGS), Rua Ramiro Barcelos, 2600-Anexo, Porto Alegre, RS, 90035-003, Brazil
| | - Bruna F Deniz
- Laboratory of Neuroprotection and Neurometabolic Diseases, Wyse's Lab, Department of Biochemistry, ICBS, Universidade Federal Do Rio Grande Do Sul (UFRGS), Rua Ramiro Barcelos, 2600-Anexo, Porto Alegre, RS, 90035-003, Brazil
| | - Carlos Alexandre Netto
- Laboratory of Neuroprotection and Neurometabolic Diseases, Wyse's Lab, Department of Biochemistry, ICBS, Universidade Federal Do Rio Grande Do Sul (UFRGS), Rua Ramiro Barcelos, 2600-Anexo, Porto Alegre, RS, 90035-003, Brazil
| | - Angela T S Wyse
- Laboratory of Neuroprotection and Neurometabolic Diseases, Wyse's Lab, Department of Biochemistry, ICBS, Universidade Federal Do Rio Grande Do Sul (UFRGS), Rua Ramiro Barcelos, 2600-Anexo, Porto Alegre, RS, 90035-003, Brazil.
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Rathi A, Kumar V, Sundar D. Insights into the potential of withanolides as Phosphodiesterase-4 (PDE4D) inhibitors. J Biomol Struct Dyn 2022; 41:2108-2117. [PMID: 35060432 DOI: 10.1080/07391102.2022.2028679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Medicinal herbs have been used as traditional medicines for centuries. The molecular mechanism of action of their bioactive molecules against various diseases or therapeutic targets is still being explored. Here, the active compounds (withanolides) of a well-known Indian medicinal herb, Ashwagandha (Withania somnifera), have been studied for their most potential therapeutic targets and their mechanism of action using ligand-based screening and receptor-based approaches. Ligand-based screening predicted the six top therapeutic targets, namely, Protein kinase C alpha (PRKCA), Protein kinase C delta (PRKCD), Protein kinase C epsilon (PRKCE), Androgenic Receptor (AR), Cycloxygenase-2 (PTGS-2) and Phosphodiesterase-4D (PDE4D). Further, when these predictions were validated using receptor-based studies, i.e. molecular docking, molecular dynamics simulation and free energy calculations, it was found that PDE4D was the most potent target for four withanolides, namely, Withaferin-A, 17-Hydroxywithaferin-A, 27-Hydroxywithanone and Withanolide-R. These compounds had a better binding affinity and similar interactions as that of an already known inhibitor (Zardaverine) of PDE4D. These results warrant further in-vitro and in-vivo investigations to examine their therapeutic potential as an inhibitor of PDE4D.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Aditya Rathi
- DAILAB, Department of Biochemical Engineering & Biotechnology, Indian Institute of Technology (IIT) Delhi, Hauz Khas, New Delhi, India
| | - Vipul Kumar
- DAILAB, Department of Biochemical Engineering & Biotechnology, Indian Institute of Technology (IIT) Delhi, Hauz Khas, New Delhi, India
| | - Durai Sundar
- DAILAB, Department of Biochemical Engineering & Biotechnology, Indian Institute of Technology (IIT) Delhi, Hauz Khas, New Delhi, India
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Kandimalla R, Chakraborty P, Vallamkondu J, Chaudhary A, Samanta S, Reddy PH, De Feo V, Dewanjee S. Counting on COVID-19 Vaccine: Insights into the Current Strategies, Progress and Future Challenges. Biomedicines 2021; 9:1740. [PMID: 34829969 PMCID: PMC8615473 DOI: 10.3390/biomedicines9111740] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/30/2021] [Accepted: 11/03/2021] [Indexed: 12/27/2022] Open
Abstract
The emergence of a novel coronavirus viz., severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in late 2019 and its subsequent substantial spread produced the coronavirus disease 2019 (COVID-19) pandemic worldwide. Given its unprecedented infectivity and pathogenicity, the COVID-19 pandemic had a devastating impact on human health, and its clinical management has been a great challenge, which has led to the development and speedy trials of several vaccine candidates against SARS-CoV-2 at an exceptional pace. As a result, several COVID-19 vaccines were made commercially available in the first half of 2021. Although several COVID-19 vaccines showed promising results, crucial insights into their epidemiology, protective mechanisms, and the propensities of reinfection are not largely reviewed. In the present report, we provided insights into the prospects of vaccination against COVID-19 and assessed diverse vaccination strategies including DNA, mRNA, protein subunits, vector-based, live attenuated, and inactivated whole/viral particle-based vaccines. Next, we reviewed major aspects of various available vaccines approved by the World Health Organization and by the local administrations to use against COVID-19. Moreover, we comprehensively assessed the success of these approved vaccines and also their untoward effects, including the possibility of reinfection. We also provided an update on the vaccines that are under development and could be promising candidates in the future. Conclusively, we provided insights into the COVID-19 vaccine epidemiology, their potency, and propensity for SARS-CoV-2 reinfection, while a careful review of their current status, strategies, success, and future challenges was also presented.
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Affiliation(s)
- Ramesh Kandimalla
- Applied Biology, CSIR-Indian Institute of Technology, Uppal Road, Tarnaka, Hyderabad 500007, Telangana, India
- Department of Biochemistry, Kakatiya Medical College, Warangal 506007, Telangana, India
| | - Pratik Chakraborty
- Advanced Pharmacognosy Research Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, West Bengal, India;
| | | | - Anupama Chaudhary
- Orinin-BioSystems, LE-52, Lotus Road 4, CHD City, Karnal 132001, Haryana, India;
| | - Sonalinandini Samanta
- Department of Dermatology (Skin & Venereology), ESIC Medical College & Hospital, Patna 801103, Bihar, India;
| | - P. Hemachandra Reddy
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA;
- Department of Neuroscience & Pharmacology, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
- Department of Neurology, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
- Public Health Department of Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
- Department of Speech, Language and Hearing Sciences, School Health Professions, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Vincenzo De Feo
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy
| | - Saikat Dewanjee
- Advanced Pharmacognosy Research Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, West Bengal, India;
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11
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Computational and in vitro experimental analyses of the anti-COVID-19 potential of Mortaparib and MortaparibPlus. Biosci Rep 2021; 41:229940. [PMID: 34647577 PMCID: PMC8527209 DOI: 10.1042/bsr20212156] [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: 09/08/2021] [Revised: 09/16/2021] [Accepted: 10/04/2021] [Indexed: 11/17/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus has become a global health emergency. Although new vaccines have been generated and being implicated, discovery and application of novel preventive and control measures are warranted. We aimed to identify compounds that may possess the potential to either block the entry of virus to host cells or attenuate its replication upon infection. Using host cell surface receptor expression (angiotensin-converting enzyme 2 (ACE2) and Transmembrane protease serine 2 (TMPRSS2)) analysis as an assay, we earlier screened several synthetic and natural compounds and identified candidates that showed ability to down-regulate their expression. Here, we report experimental and computational analyses of two small molecules, Mortaparib and MortaparibPlus that were initially identified as dual novel inhibitors of mortalin and PARP-1, for their activity against SARS-CoV-2. In silico analyses showed that MortaparibPlus, but not Mortaparib, stably binds into the catalytic pocket of TMPRSS2. In vitro analysis of control and treated cells revealed that MortaparibPlus caused down-regulation of ACE2 and TMPRSS2; Mortaparib did not show any effect. Furthermore, computational analysis on SARS-CoV-2 main protease (Mpro) that also predicted the inhibitory activity of MortaparibPlus. However, cell-based antiviral drug screening assay showed 30-60% viral inhibition in cells treated with non-toxic doses of either MortaparibPlus or Mortaparib. The data suggest that these two closely related compounds possess multimodal anti-COVID-19 activities. Whereas MortaparibPlus works through direct interactions/effects on the host cell surface receptors (ACE2 and TMPRSS2) and the virus protein (Mpro), Mortaparib involves independent mechanisms, elucidation of which warrants further studies.
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12
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Zafar H, Atif M, Atia-tul-Wahab, Choudhary MI. Fucosyltransferase 2 inhibitors: Identification via docking and STD-NMR studies. PLoS One 2021; 16:e0257623. [PMID: 34648519 PMCID: PMC8516197 DOI: 10.1371/journal.pone.0257623] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 09/05/2021] [Indexed: 12/18/2022] Open
Abstract
Fucosyltransferase 2 (FUT2) catalyzes the biosynthesis of A, B, and H antigens and other important glycans, such as (Sialyl Lewisx) sLex, and (Sialyl Lewisy) sLey. The production of these glycans is increased in various cancers, hence to design and develop specific inhibitors of FUT2 is a therapeutic strategy. The current study was designed to identify the inhibitors for FUT2. In silico screening of 300 synthetic compounds was performed. Molecular docking studies highlighted the interactions of ligands with critical amino acid residues, present in the active site of FUT2. The epitope mapping in ligands was performed using the STD-NMR experiments to identify the interactions between ligands, and receptor protein. Finally, we have identified 5 lead compounds 4, 5, 26, 27, and 28 that can be studied for further development as cancer therapeutic agents.
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Affiliation(s)
- Humaira Zafar
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Muhammad Atif
- H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Atia-tul-Wahab
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - M. Iqbal Choudhary
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
- H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
- Faculty of Science and Technology, Department of Chemistry, Universitas Airlangga, Komplek Campus C, Surabaya, Indonesia
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13
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Yin MZ, Zhu QW, Lü X. Parameter estimation of the incubation period of COVID-19 based on the doubly interval-censored data model. NONLINEAR DYNAMICS 2021; 106:1347-1358. [PMID: 34177117 PMCID: PMC8211977 DOI: 10.1007/s11071-021-06587-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 05/26/2021] [Indexed: 05/09/2023]
Affiliation(s)
- Ming-Ze Yin
- Department of Mathematics, Beijing Jiaotong University, Beijing, 100044 China
| | - Qing-Wen Zhu
- Department of Mathematics, Beijing Jiaotong University, Beijing, 100044 China
| | - Xing Lü
- Department of Mathematics, Beijing Jiaotong University, Beijing, 100044 China
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14
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Emerging COVID-19 Neurological Manifestations: Present Outlook and Potential Neurological Challenges in COVID-19 Pandemic. Mol Neurobiol 2021; 58:4694-4715. [PMID: 34169443 PMCID: PMC8224263 DOI: 10.1007/s12035-021-02450-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 06/07/2021] [Indexed: 02/06/2023]
Abstract
The unremitting coronavirus disease 2019 (COVID-19) pandemic caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) marked a year-long phase of public health adversaries and has severely compromised healthcare globally. Early evidence of COVID-19 noted its impact on the pulmonary and cardiovascular functions, while multiple studies in recent time shed light on its substantial neurological complications, though a comprehensive understanding of the cause(s), the mechanism(s), and their neuropathological outcomes is scarce. In the present review, we conferred evidence of neurological complications in COVID-19 patients and shed light on the SARS-CoV-2 infection routes including the hematogenous, direct/neuronal, lymphatic tissue or cerebrospinal fluid, or infiltration through infected immune cells, while the underlying mechanism of SARS-CoV-2 invasion to the central nervous system (CNS) was also discussed. In an up-to-date manner, we further reviewed the impact of COVID-19 in developing diverse neurologic manifestations associated with CNS, peripheral nervous system (PNS), skeletal muscle, and also pre-existing neurological diseases, including Alzheimer's disease, Parkinson's disease, multiple sclerosis, epilepsy, and myasthenia gravis. Furthermore, we discussed the involvement of key factors including age, sex, comorbidity, and disease severity in exacerbating the neurologic manifestations in COVID-19 patients. An outlook of present therapeutic strategies and state of existing challenges in COVID-19 management was also accessed. Conclusively, the present report provides a comprehensive review of COVID-19-related neurological complications and emphasizes the need for their early clinical management in the ongoing COVID-19 pandemic.
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15
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Kalra RS, Dhanjal JK, Meena AS, Kalel VC, Dahiya S, Singh B, Dewanjee S, Kandimalla R. COVID-19, Neuropathology, and Aging: SARS-CoV-2 Neurological Infection, Mechanism, and Associated Complications. Front Aging Neurosci 2021; 13:662786. [PMID: 34149397 PMCID: PMC8209245 DOI: 10.3389/fnagi.2021.662786] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 05/05/2021] [Indexed: 01/08/2023] Open
Abstract
The spectrum of health complications instigated by coronavirus disease 2019 (COVID-19, caused by the novel severe acute respiratory syndrome coronavirus 2 or SARS-CoV-2) pandemic has been diverse and complex. Besides the evident pulmonary and cardiovascular threats, accumulating clinical data points to several neurological complications, which are more common in elderly COVID-19 patients. Recent pieces of evidence have marked events of neuro infection and neuroinvasion, producing several neurological complications in COVID-19 patients; however, a systematic understanding of neuro-pathophysiology and manifested neurological complications, more specifically in elderly COVID-19 patients is largely elusive. Since the elderly population gradually develops neurological disorders with aging, COVID-19 inevitably poses a higher risk of neurological manifestations to the aged patients. In this report, we reviewed SARS-CoV-2 infection and its role in neurological manifestations with an emphasis on the elderly population. We reviewed neuropathological events including neuroinfection, neuroinvasion, and their underlying mechanisms affecting neuromuscular, central- and peripheral- nervous systems. We further assessed the imminent neurological challenges in the COVID-19 exposed population, post-SARS-CoV-2-infection. Given the present state of clinical preparedness, the emerging role of AI and machine learning was also discussed concerning COVID-19 diagnostics and its management. Taken together, the present review summarizes neurological outcomes of SARS-CoV-2 infection and associated complications, specifically in elderly patients, and underlines the need for their clinical management in advance.
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Affiliation(s)
- Rajkumar Singh Kalra
- AIST-INDIA DAILAB, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Jaspreet Kaur Dhanjal
- Department of Computational Biology, Indraprastha Institute of Information Technology Delhi, Okhla Industrial Estate, New Delhi, India
| | - Avtar Singh Meena
- CSIR-Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India
| | - Vishal C. Kalel
- Department of Systems Biochemistry, Institute of Biochemistry and Pathobiochemistry, Faculty of Medicine, Ruhr-University Bochum, Bochum, Germany
| | - Surya Dahiya
- Conservative Dentistry and Endodontics, Maharishi Markandeshwar College of Dental Sciences and Research, Ambala, India
| | - Birbal Singh
- ICAR-Indian Veterinary Research Institute (IVRI), Regional Station, Palampur, India
| | - Saikat Dewanjee
- Advanced Pharmacognosy Research Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Ramesh Kandimalla
- Applied Biology, CSIR-Indian Institute of Chemical Technology (IICT), Hyderabad, India
- Department of Biochemistry, Kakatiya Medical College, Warangal, India
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