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Dhawale SA, Mahajan S, Pandit M, Gawale S, Ghodke M, Tapadiya G. Molecular docking and molecular dynamic simulation-based phytoconstituents against SARS-CoV-2 with dual inhibition of the primary protease targets. Nat Prod Res 2024:1-6. [PMID: 38517217 DOI: 10.1080/14786419.2024.2330526] [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: 05/12/2023] [Accepted: 02/28/2024] [Indexed: 03/23/2024]
Abstract
A novel coronavirus has caused major health problems and is spreading globally. The main protease enzyme plays a significant role in the number of copies of ss-RNA produced during the proteolytic cleavage of polypeptides. This work aims to find possible dual inhibitors of the 3-Chymotrypsin-like proteases PDB-6W63 and 6LU7 which increase efficiency and faster inhibition activity. By using an in-silico technique, polyphenols are molecularly docked against these targets to inhibit protease enzymes. Some polyphenols, such as pelargonidin and naringin, have significant dual inhibition characteristics with remarkable binding affinities with active scaffolds of both proteins, which have important ADMET parameters. These organic molecules are strongly bonded with amino acids of protein via mostly hydrogen bonding. These polyphenols also have outstanding docking scores and MMGBSA energies. The validity of the docking score was evaluated using a molecular dynamics simulation that assessed the stability of the complex. With the aid of computer-aided drug design, we hypothesise that the dual inhibition of compounds pelargonidin and naringin could effectively and potentially oppose SARS-CoV-2.
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Affiliation(s)
- Sachin A Dhawale
- Department of Pharmaceutical Chemistry, Shreeyash Institute of Pharmaceutical Education and Research, Aurangabad, Maharashtra, India
| | - Sadhana Mahajan
- Department of Pharmaceutical Chemistry, K.B.H.S.S Trusts Institute of Pharmacy, Nashik, Maharashtra, India
| | - Madhuri Pandit
- Department of Pharmaceutical Chemistry, Shreeyash Institute of Pharmaceutical Education and Research, Aurangabad, Maharashtra, India
| | - Sachin Gawale
- Department of Pharmaceutical Chemistry, Shreeyash Institute of Pharmaceutical Education and Research, Aurangabad, Maharashtra, India
| | - Mangesh Ghodke
- Department of Pharmaceutical Chemistry, Shreeyash Institute of Pharmaceutical Education and Research, Aurangabad, Maharashtra, India
| | - Ganesh Tapadiya
- Department of Pharmaceutical Chemistry, Shreeyash Institute of Pharmaceutical Education and Research, Aurangabad, Maharashtra, India
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Assefa T, Tesso H, Ramachandran VP, Guta L, Demissie TB, Ombito JO, Eswaramoorthy R, Melaku Y. In Silico Molecular Docking Analysis, Cytotoxicity, and Antibacterial Activities of Constituents of Fruits of Cucumis dipsaceus. ACS OMEGA 2024; 9:1945-1955. [PMID: 38222496 PMCID: PMC10785779 DOI: 10.1021/acsomega.3c08866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 11/29/2023] [Accepted: 11/30/2023] [Indexed: 01/16/2024]
Abstract
Cucumis dipsaceus (Cucurbitaceae) is a plant traditionally used against diarrhea, teeth-ach, wounds, stomach ache, meningitis, and cancer. The extracts of C. dipsaceus after silica gel column chromatography gave nine compounds identified using spectroscopic methods such as hexacosane (1), octadecane (2), 17-(-5-ethyl-2,6-dihydroxy-6-methylhept-3-en-2-yl)-9-(hydroxymethyl)-13-methylcyclopenta[α]phenanthren-3-ol (3), erythrodiol (4), (9,12)-propyl icosa-9,12-dienoate (5), α-spinasterol (6), 16-dehydroxycucurbitacin (7), cucurbitacin D (8), and 23,24-dihydroisocucurbitacin D (9). Compounds 3 and 4 are new to the genus Cucumis. α-Spinasterol showed better inhibition zone diameter = 13.67 ± 0.57, 15.00 ± 0.10, and 13.33 ± 0.57 mm against Escherichia coli, Pseudomonas aeruginosa, and Streptococcus pyogenes compared with the other tested samples. α-Spinasterol (-8.0 kcal/mol) and 3 (-7.6 kcal/mol) displayed high binding affinity against DNA Gyrase compared to ciprofloxacin (-7.3 kcal/mol). α-Spinasterol and 16-dehydroxycucurbitacin showed better binding affinity against protein kinase. The cytotoxicity results revealed that the EtOAc extract showed the highest potency with IC50 = 16.05 μg/mL. 16-Dehydroxycucurbitacin showed a higher binding affinity (-7.7 kcal/mol) against human topoisomerase IIβ than etoposide. The cytotoxicity and antibacterial activities and in silico molecular docking analysis displayed by the constituents corroborate the traditional use of the plant against bacteria and cancer.
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Affiliation(s)
- Teshale Assefa
- Department
of Applied Chemistry, Adama Science and
Technology University, P.O. Box, Adama 1888, Ethiopia
| | - Hailemichael Tesso
- Department
of Applied Chemistry, Adama Science and
Technology University, P.O. Box, Adama 1888, Ethiopia
| | | | - Leta Guta
- Department
of Applied Biology, Adama Science and Technology
University, P.O. Box, Adama 1888, Ethiopia
| | - Taye B. Demissie
- Department
of Chemistry, University of Botswana, Gaborone P/Bag 00704, Botswana
| | - Japheth O. Ombito
- Department
of Chemistry, University of Botswana, Gaborone P/Bag 00704, Botswana
| | - Rajalakshmanan Eswaramoorthy
- Department
of Biomaterials, S Aveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences
(SIMATS), Saveetha University, Chennai 600 077, India
| | - Yadessa Melaku
- Department
of Applied Chemistry, Adama Science and
Technology University, P.O. Box, Adama 1888, Ethiopia
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3
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Zieniuk B, Pawełkowicz M. Recent Advances in the Application of Cucurbitacins as Anticancer Agents. Metabolites 2023; 13:1081. [PMID: 37887406 PMCID: PMC10608718 DOI: 10.3390/metabo13101081] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/08/2023] [Accepted: 10/12/2023] [Indexed: 10/28/2023] Open
Abstract
Cucurbitacins are tetracyclic triterpenoid secondary metabolites, widely distributed in the Cucurbitaceae family. These bitter-tasting compounds act primarily as defense mechanisms against external injuries, and thus against herbivores, and furthermore, they have also found use in folk medicine in the treatment of various diseases. Many studies have acknowledged significant biological activities of cucurbitacins, such as antioxidant and anti-inflammatory activities, antimicrobial properties, or antitumor potential. Overall, cucurbitacins have the ability to inhibit cell proliferation and induce apoptosis in various cancer cell lines. Both in vitro and in vivo studies were performed to evaluate the anticancer activity of varied cucurbitacins. Cucurbitacins offer a promising avenue for future cancer treatment strategies, and their diverse mechanisms of action make them attractive candidates for further investigation. The aim of the present study is to shed light on the chemical diversity of this group of compounds by providing the sources of origin of selected compounds and their chemical structure, as well as insight into their anticancer potential. In addition, within this paper molecular targets for cucurbitacins and signalling pathways important for cancer cell proliferation and/or survival that are affected by the described class of compounds have been presented.
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Affiliation(s)
- Bartłomiej Zieniuk
- Department of Chemistry, Institute of Food Sciences, Warsaw University of Life Sciences, 02-776 Warsaw, Poland;
| | - Magdalena Pawełkowicz
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences, 02-776 Warsaw, Poland
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Tuli HS, Rath P, Chauhan A, Ranjan A, Ramniwas S, Sak K, Aggarwal D, Kumar M, Dhama K, Lee EHC, Yap KCY, Capinpin SM, Kumar AP. Cucurbitacins as Potent Chemo-Preventive Agents: Mechanistic Insight and Recent Trends. Biomolecules 2022; 13:biom13010057. [PMID: 36671442 PMCID: PMC9855938 DOI: 10.3390/biom13010057] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 12/29/2022] Open
Abstract
Cucurbitacins constitute a group of cucumber-derived dietary lipids, highly oxidized tetracyclic triterpenoids, with potential medical uses. These compounds are known to interact with a variety of recognized cellular targets to impede the growth of cancer cells. Accumulating evidence has suggested that inhibition of tumor cell growth via induction of apoptosis, cell-cycle arrest, anti-metastasis and anti-angiogenesis are major promising chemo-preventive actions of cucurbitacins. Cucurbitacins may be a potential choice for investigations of synergism with other drugs to reverse cancer cells' treatment resistance. The detailed molecular mechanisms underlying these effects include interactions between cucurbitacins and numerous cellular targets (Bcl-2/Bax, caspases, STAT3, cyclins, NF-κB, COX-2, MMP-9, VEGF/R, etc.) as well as control of a variety of intracellular signal transduction pathways. The current study is focused on the efforts undertaken to find possible molecular targets for cucurbitacins in suppressing diverse malignant processes. The review is distinctive since it presents all potential molecular targets of cucurbitacins in cancer on one common podium.
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Affiliation(s)
- Hardeep Singh Tuli
- Department of Biotechnology, Maharishi Markandeshwar Engineering College, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala 133207, India
- Correspondence: (H.S.T.); (A.P.K.)
| | - Prangya Rath
- Amity Institute of Environmental Sciences, Amity University, Noida 201303, India
| | - Abhishek Chauhan
- Amity Institute of Environmental Toxicology, Safety and Management, Amity University, Noida 201303, India
| | - Anuj Ranjan
- Academy of Biology and Biotechnology, Southern Federal University, 344090 Rostov-on-Don, Russia
| | - Seema Ramniwas
- University Centre for Research and Development, University Institute of Pharmaceutical Sciences, Chandigarh University, Mohali 140413, India
| | | | - Diwakar Aggarwal
- Department of Biotechnology, Maharishi Markandeshwar Engineering College, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala 133207, India
| | - Manoj Kumar
- Department of Chemistry, Maharishi Markandeshwar University Sadopur, Ambala 134007, India
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Bareilly 243122, India
| | - E Hui Clarissa Lee
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore
- NUS Centre for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore
| | - Kenneth Chun-Yong Yap
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore
- NUS Centre for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore
| | - Sharah Mae Capinpin
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore
- NUS Centre for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore
| | - Alan Prem Kumar
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore
- NUS Centre for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore
- Correspondence: (H.S.T.); (A.P.K.)
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Delgado-Tiburcio EE, Cadena-Iñiguez J, Santiago-Osorio E, Ruiz-Posadas LDM, Castillo-Juárez I, Aguiñiga-Sánchez I, Soto-Hernández M. Pharmacokinetics and Biological Activity of Cucurbitacins. Pharmaceuticals (Basel) 2022; 15:1325. [PMID: 36355498 PMCID: PMC9696414 DOI: 10.3390/ph15111325] [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] [Received: 07/11/2022] [Revised: 10/01/2022] [Accepted: 10/20/2022] [Indexed: 11/04/2023] Open
Abstract
Cucurbitacins are a class of secondary metabolites initially isolated from the Cucurbitaceae family. They are important for their analgesic, anti-inflammatory, antimicrobial, antiviral, and anticancer biological actions. This review addresses pharmacokinetic parameters recently reported, including absorption, metabolism, distribution, and elimination phases of cucurbitacins. It includes recent studies of the molecular mechanisms of the biological activity of the most studied cucurbitacins and some derivatives, especially their anticancer capacity, to propose the integration of the pharmacokinetic profiles of cucurbitacins and the possibilities of their use. The main botanical genera and species of American origin that have been studied, and others whose chemo taxonomy makes them essential sources for the extraction of these metabolites, are summarized.
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Affiliation(s)
| | - Jorge Cadena-Iñiguez
- Innovation in Natural Resource Management, Postgraduate College, Campus San Luis Potosí, Salinas de Hidalgo, San Luis Potosí 78622, Mexico
| | - Edelmiro Santiago-Osorio
- Hematopoiesis and Leukemia Laboratory, Research Unit on Cell Differentiation and Cancer, FES Zaragoza, National Autonomous University of Mexico, Mexico City 09230, Mexico
| | - Lucero Del Mar Ruiz-Posadas
- Botany Department, Postgraduate College, Campus Montecillo, km 36.5 Carretera México-Texcoco, Texcoco 56230, Mexico
| | - Israel Castillo-Juárez
- Botany Department, Postgraduate College, Campus Montecillo, km 36.5 Carretera México-Texcoco, Texcoco 56230, Mexico
| | - Itzen Aguiñiga-Sánchez
- Hematopoiesis and Leukemia Laboratory, Research Unit on Cell Differentiation and Cancer, FES Zaragoza, National Autonomous University of Mexico, Mexico City 09230, Mexico
- Department of Biomedical Sciences, School of Medicine, FES Zaragoza, National Autonomous University of Mexico, Mexico City 09230, Mexico
| | - Marcos Soto-Hernández
- Botany Department, Postgraduate College, Campus Montecillo, km 36.5 Carretera México-Texcoco, Texcoco 56230, Mexico
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Kapoor N, Ghorai SM, Khuswaha PK, Bandichhor R, Brogi S. Butein as a potential binder of human ACE2 receptor for interfering with SARS-CoV-2 entry: a computer-aided analysis. J Mol Model 2022; 28:270. [PMID: 36001177 PMCID: PMC9399596 DOI: 10.1007/s00894-022-05270-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 08/12/2022] [Indexed: 12/24/2022]
Abstract
Natural products have been included in our dietary supplements and have been shown to have numerous therapeutic properties. With the looming danger of many zoonotic agents and novel emerging pathogens mainly of viral origin, many researchers are launching various clinical trials, testing these compounds for their antiviral activity. The present work deals with some of the available natural compounds from the literature that have demonstrated activity in counteracting pathogen infections. Accordingly, we screened, using in silico methods, this subset of natural compounds for searching potential drug candidates able to interfere in the recognition of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein and its target human angiotensin-converting enzyme 2 (hACE2) receptor, leading to the viral entry. Disrupting that recognition is crucial for slowing down the entrance of viral particles into host cells. The selected group of natural products was examined, and their interaction profiles against the host cell target protein ACE2 were studied at the atomic level. Based on different computer-based procedures including molecular docking, physicochemical property evaluation, and molecular dynamics, butein was identified as a potential hit molecule able to bind the hACE2 receptor. The results indicate that herbal compounds can be effective for providing possible therapeutics for treating and managing coronavirus disease 2019 (COVID-19) infection.
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Affiliation(s)
- Neha Kapoor
- Department of Chemistry, Hindu College, University of Delhi, Delhi, 110007, India.
| | - Soma Mondal Ghorai
- Department of Zoology, Hindu College, University of Delhi, Delhi, 110007, India
| | - Prem Kumar Khuswaha
- Integrated Product Development, Innovation Plaza, Dr. Reddy's Laboratories Ltd, Bachupally, Quthbullapur, Hyderabad, 500090, Telangana, India
| | - Rakeshwar Bandichhor
- Integrated Product Development, Innovation Plaza, Dr. Reddy's Laboratories Ltd, Bachupally, Quthbullapur, Hyderabad, 500090, Telangana, India
| | - Simone Brogi
- Department of Pharmacy, University of Pisa, Via Bonanno, 6, 56126, Pisa, Italy.
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Goswami P, Chatterjee D, Ghosh S, Paira K, Das S. Balanced cytokine upregulation by diluted ethanolic extract of Bryonia alba in Delta SARS-CoV-2 Spike protein RBD-induced pathogenesis in Gallus gallus embryo. BULLETIN OF THE NATIONAL RESEARCH CENTRE 2022; 46:169. [PMID: 35729949 PMCID: PMC9188851 DOI: 10.1186/s42269-022-00856-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 05/31/2022] [Indexed: 06/15/2023]
Abstract
Background Bryonia alba extract is a well-known drug which is being utilized as phytomedicines and homoeopathic preparations since more than two centuries. This medicine is frequently used in clinical practice for flu-like conditions, respiratory tract infections, and gastrointestinal diseases, as evidenced by old literature and historical records. The plant contains Bryonicin, Bryonolic acid, Bryodin, Cucurbitacin, etc. The alkaloids in Bryonia alba have been discovered to be a powerful heme-oxygenase-1 inhibitor, which could help reduce oxidative stress during SARS-CoV-2 pathogenesis. During three waves of SARS-CoV-2, extracts of Bryonia alba were used; however, the actual scientific explanation for its mechanism of action is still unknown. In this experiment, we studied cytokine changes by diluted Bryonia alba extract in Delta SARS-CoV-2 spike protein RBD-induced pathogenesis, in fertilized chick (Gallus gallus domesticus) embryos. Results The recombinant Delta SARS-CoV-2 spike RBD protein was inoculated in 14-day-old chick (Gallus gallus domesticus) embryos along with control, pre-, and post-treatment sets with diluted Bryonia extract. After 48 h, allantoic fluids were collected and stored at - 20 °C for study of different cytokines. Histological changes of the liver were also studied in each animal. Diluted Bryonia extract upregulated IFN-α and IL-10 markedly. In pre-treatment set, IFN-α, IL-8, IL-10, and IL-1β were markedly decreased, while in the post-treatment set IL-6, IL-10, IL-8, and TGFβ1 were significantly decreased, with a tendency of more anti-inflammatory surge than pro-inflammatory cytokines. Conclusions This experiment indicated an immunomodulatory role of diluted ethanolic extract of Bryonia particularly in the post-treatment set, decreasing pro-inflammatory cytokines with beneficial effect.
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Affiliation(s)
- Pritam Goswami
- West Bengal University of Health Sciences, Kolkata, India
| | - Debasmita Chatterjee
- Genetic Research Laboratory, Heritage Institute of Technology, Kolkata, 700 107 India
| | - Sayak Ghosh
- West Bengal University of Health Sciences, Kolkata, India
| | - Krishnendu Paira
- Genetic Research Laboratory, Heritage Institute of Technology, Kolkata, 700 107 India
| | - Satadal Das
- Genetic Research Laboratory, Heritage Institute of Technology, Kolkata, 700 107 India
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Omer SE, Ibrahim TM, Krar OA, Ali AM, Makki AA, Ibraheem W, Alzain AA. Drug repurposing for SARS-CoV-2 main protease: Molecular docking and molecular dynamics investigations. Biochem Biophys Rep 2022; 29:101225. [PMID: 35128086 PMCID: PMC8801302 DOI: 10.1016/j.bbrep.2022.101225] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 01/18/2022] [Accepted: 01/27/2022] [Indexed: 12/23/2022] Open
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Ma LL, Liu HM, Liu XM, Yuan XY, Xu C, Wang F, Lin JZ, Xu RC, Zhang DK. Screening S protein - ACE2 blockers from natural products: Strategies and advances in the discovery of potential inhibitors of COVID-19. Eur J Med Chem 2021; 226:113857. [PMID: 34628234 PMCID: PMC8489279 DOI: 10.1016/j.ejmech.2021.113857] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/11/2021] [Accepted: 09/15/2021] [Indexed: 02/09/2023]
Abstract
The Coronavirus disease, 2019 (COVID-19) is caused by severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2), which poses a major threat to human life and health. Given its continued development, limiting the spread of COVID-19 in the population remains a challenging task. Currently, multiple therapies are being tried around the world to deal with SARS-CoV-2 infection, and a variety of studies have shown that natural products have a significant effect on COVID-19 patients. The combination of SARS-CoV-2 S protein with Angiotensin converting enzyme II(ACE2) of host cell to promote membrane fusion is an initial critical step for SARS-CoV-2 infection. Therefore, screening natural products that inhibit the binding of SARS-CoV-2 S protein and ACE2 also provides a feasible strategy for the treatment of COVID-19. Establishment of high throughput screening model is an important basis and key technology for screening S protein-ACE2 blockers. Based on this, the molecular structures of SARS-CoV-2 and ACE2 and their processes in the life cycle of SARS-CoV-2 and host cell infection were firstly reviewed in this paper, with emphasis on the methods and techniques of screening S protein-ACE2 blockers, including Virtual Screening (VS), Surface Plasmon Resonance (SPR), Biochromatography, Biotin-avidin with Enzyme-linked Immunosorbent assay and Gene Chip Technology. Furthermore, the technical principle, advantages and disadvantages and application scope were further elaborated. Combined with the application of the above screening technologies in S protein-ACE2 blockers, a variety of natural products, such as flavonoids, terpenoids, phenols, alkaloids, were summarized, which could be used as S protein-ACE2 blockers, in order to provide ideas for the efficient discovery of S protein-ACE2 blockers from natural sources and contribute to the development of broad-spectrum anti coronavirus drugs.
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Affiliation(s)
- Le-le Ma
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, PR China
| | - Hui-Min Liu
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, PR China
| | - Xue-Mei Liu
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, PR China
| | - Xiao-Yu Yuan
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, PR China
| | - Chao Xu
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, PR China
| | - Fang Wang
- Key Laboratory of Modern Chinese Medicine Preparation of Ministry of Education, Jiangxi University of Traditional Chinese Medicine Central Laboratory, Nanchang, 330000, PR China
| | - Jun-Zhi Lin
- TCM Regulating Metabolic Diseases Key Laboratory of Sichuan Province, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610072, PR China.
| | - Run-Chun Xu
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, PR China.
| | - Ding-Kun Zhang
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, PR China.
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Yueniwati Y, Rizki Syaban MF, Faratisha IFD, Yunita KC, Kurniawan DB, Putra GFA, Erwan NE. Molecular Docking Approach of Natural Compound from Herbal Medicine in Java against Severe Acute Respiratory Syndrome Coronavirus-2 Receptor. Open Access Maced J Med Sci 2021. [DOI: 10.3889/oamjms.2021.6963] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Indonesia's diversity of natural resources presents an intriguing opportunity for the exploration of potential herbal medicines. Numerous compounds, both purified and crude, have been reported to exhibit antiviral activity. The ACE-2 receptor may be a therapeutic target for SARS-CoV-2 infection. We used a search engine to search for herbal medicines with ACE-2 inhibitory activity to predict the potential inhibition of natural compounds (i.e., theaflavin, deoxypodophyllotoxin, gallocatechin, allicin, quercetin, annonamine, Curcumin, 6-gingerol, and cucurbitacin B) to SARS-CoV2 – ACE-2 complex. We performed molecular docking analysis using the ACE-2 protein target from Protein Data Bank. Protein stabilization was carried out to adjust to the body's physiology, carried out using Pymol by removing water atoms and adding hydrogen atoms. Ligands of active compounds from natural resources were selected and downloaded from the PubChem database, then optimized by Pymol software. The complexes of the tested ligand compounds and ACE-2 receptors, which have a bond strength smaller than the control were selected for analysis. Theaflavin, Deoxypodophyllotoxin, Gallocatechin, Curcumin, and Cucurbitacin B had a strong bond affinity than the control ligands. Based on our data, deoxypodophylotoxin and Curcumin had the same interaction amino acid residus compare to the control ligand. This study concludes that deoxypodophyllotoxin and Curcumin have the greatest potential to inhibit the formation of the SARS-Cov2-ACE-2 complex; additionally, these compounds exhibit favorable pharmacological and pharmacodynamic properties. It is suggested that additional research be conducted to determine the biological effects of deoxypodopyllotoxin and Curcumin on ACE-2 receptors.
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González-Paz L, Hurtado-León ML, Lossada C, Fernández-Materán FV, Vera-Villalobos J, Loroño M, Paz JL, Jeffreys L, Alvarado YJ. Comparative study of the interaction of ivermectin with proteins of interest associated with SARS-CoV-2: A computational and biophysical approach. Biophys Chem 2021; 278:106677. [PMID: 34428682 PMCID: PMC8373590 DOI: 10.1016/j.bpc.2021.106677] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 08/13/2021] [Accepted: 08/15/2021] [Indexed: 01/18/2023]
Abstract
The SARS-CoV-2 pandemic has accelerated the study of existing drugs. The mixture of homologs called ivermectin (avermectin-B1a [HB1a] + avermectin-B1b [HB1b]) has shown antiviral activity against SARS-CoV-2 in vitro. However, there are few reports on the behavior of each homolog. We investigated the interaction of each homolog with promising targets of interest associated with SARS-CoV-2 infection from a biophysical and computational-chemistry perspective using docking and molecular dynamics. We observed a differential behavior for each homolog, with an affinity of HB1b for viral structures, and of HB1a for host structures considered. The induced disturbances were differential and influenced by the hydrophobicity of each homolog and of the binding pockets. We present the first comparative analysis of the potential theoretical inhibitory effect of both avermectins on biomolecules associated with COVID-19, and suggest that ivermectin through its homologs, has a multiobjective behavior.
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Affiliation(s)
- Lenin González-Paz
- Universidad del Zulia (LUZ), Facultad Experimental de Ciencias (FEC), Departamento de Biología, Laboratorio de Genética y Biología Molecular (LGBM), 4001 Maracaibo, Venezuela; Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Estudios Botánicos y Agroforestales (CEBA), Laboratorio de Protección Vegetal (LPV), 4001 Maracaibo, Venezuela.
| | - María Laura Hurtado-León
- Universidad del Zulia (LUZ), Facultad Experimental de Ciencias (FEC), Departamento de Biología, Laboratorio de Genética y Biología Molecular (LGBM), 4001 Maracaibo, Venezuela
| | - Carla Lossada
- Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Investigación y Tecnología de Materiales (CITeMA), Laboratorio de Caracterización Molecular y Biomolecular, 4001 Maracaibo, Venezuela
| | - Francelys V Fernández-Materán
- Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Investigación y Tecnología de Materiales (CITeMA), Laboratorio de Caracterización Molecular y Biomolecular, 4001 Maracaibo, Venezuela
| | - Joan Vera-Villalobos
- Facultad de Ciencias Naturales y Matemáticas, Departamento de Química y Ciencias Ambientales, Laboratorio de Análisis Químico Instrumental (LAQUINS), Escuela Superior Politécnica del Litoral, Guayaquil, Ecuador
| | - Marcos Loroño
- Departamento Académico de Química Analítica e Instrumental, Facultad de Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - J L Paz
- Departamento Académico de Química Inorgánica, Facultad de Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Laura Jeffreys
- Centre for Drugs and Diagnostics, Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Ysaias J Alvarado
- Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Investigación y Tecnología de Materiales (CITeMA), Laboratorio de Caracterización Molecular y Biomolecular, 4001 Maracaibo, Venezuela.
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González-Paz L, Hurtado-León ML, Lossada C, Fernández-Materán FV, Vera-Villalobos J, Loroño M, Paz JL, Jeffreys L, Alvarado YJ. Structural deformability induced in proteins of potential interest associated with COVID-19 by binding of homologues present in ivermectin: Comparative study based in elastic networks models. J Mol Liq 2021; 340:117284. [PMID: 34421159 PMCID: PMC8367659 DOI: 10.1016/j.molliq.2021.117284] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 08/10/2021] [Accepted: 08/12/2021] [Indexed: 12/24/2022]
Abstract
The COVID-19 pandemic has accelerated the study of the potential of multi-target drugs (MTDs). The mixture of homologues called ivermectin (avermectin-B1a + avermectin-B1b) has been shown to be a MTD with potential antiviral activity against SARS-CoV-2 in vitro. However, there are few reports on the effect of each homologue on the flexibility and stiffness of proteins associated with COVID-19, described as ivermectin targets. We observed that each homologue was stably bound to the proteins studied and was able to induce detectable changes with Elastic Network Models (ENM). The perturbations induced by each homologue were characteristic of each compound and, in turn, were represented by a disruption of native intramolecular networks (interactions between residues). The homologues were able to slightly modify the conformation and stability of the connection points between the Cα atoms of the residues that make up the structural network of proteins (nodes), compared to free proteins. Each homologue was able to modified differently the distribution of quasi-rigid regions of the proteins, which could theoretically alter their biological activities. These results could provide a biophysical-computational view of the potential MTD mechanism that has been reported for ivermectin.
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Affiliation(s)
- Lenin González-Paz
- Universidad del Zulia (LUZ), Facultad Experimental de Ciencias (FEC), Departamento de Biología. Laboratorio de Genética y Biología Molecular (LGBM), 4001 Maracaibo, Republica Bolivariana de Venezuela.,Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Estudios Botánicos y Agroforestales (CEBA), Laboratorio de Protección Vegetal (LPV), 4001 Maracaibo, Republica Bolivariana de Venezuela
| | - María Laura Hurtado-León
- Universidad del Zulia (LUZ), Facultad Experimental de Ciencias (FEC), Departamento de Biología. Laboratorio de Genética y Biología Molecular (LGBM), 4001 Maracaibo, Republica Bolivariana de Venezuela
| | - Carla Lossada
- Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Investigación y Tecnología de Materiales (CITeMA), Laboratorio de Caracterización Molecular y Biomolecular, 4001 Maracaibo, Republica Bolivariana de Venezuela
| | - Francelys V Fernández-Materán
- Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Investigación y Tecnología de Materiales (CITeMA), Laboratorio de Caracterización Molecular y Biomolecular, 4001 Maracaibo, Republica Bolivariana de Venezuela
| | - Joan Vera-Villalobos
- Facultad de Ciencias Naturales y Matemáticas, Departamento de Química y Ciencias Ambientales, Laboratorio de Análisis Químico Instrumental (LAQUINS), Escuela Superior Politécnica del Litoral, Guayaquil, Ecuador
| | - Marcos Loroño
- Departamento Académico de Química Analítica e Instrumental, Facultad de Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos, Lima, Perú
| | - J L Paz
- Departamento Académico de Química Inorgánica, Facultad de Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos, Lima, Perú
| | - Laura Jeffreys
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Ysaias J Alvarado
- Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Investigación y Tecnología de Materiales (CITeMA), Laboratorio de Caracterización Molecular y Biomolecular, 4001 Maracaibo, Republica Bolivariana de Venezuela
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Mengist HM, Dilnessa T, Jin T. Structural Basis of Potential Inhibitors Targeting SARS-CoV-2 Main Protease. Front Chem 2021; 9:622898. [PMID: 33889562 PMCID: PMC8056153 DOI: 10.3389/fchem.2021.622898] [Citation(s) in RCA: 183] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/04/2021] [Indexed: 12/23/2022] Open
Abstract
The Coronavirus disease-19 (COVID-19) pandemic is still devastating the world causing significant social, economic, and political chaos. Corresponding to the absence of globally approved antiviral drugs for treatment and vaccines for controlling the pandemic, the number of cases and/or mortalities are still rising. Current patient management relies on supportive treatment and the use of repurposed drugs as an indispensable option. Of a crucial role in the viral life cycle, ongoing studies are looking for potential inhibitors to the main protease (Mpro) of severe acute respiratory syndrome Coronavirus -2 (SARS-CoV-2) to tackle the pandemic. Although promising results have been achieved in searching for drugs inhibiting the Mpro, work remains to be done on designing structure-based improved drugs. This review discusses the structural basis of potential inhibitors targeting SARS-CoV-2 Mpro, identifies gaps, and provides future directions. Further, compounds with potential Mpro based antiviral activity are highlighted.
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Affiliation(s)
- Hylemariam Mihiretie Mengist
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of innate immunity and chronic disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Department of Medical Laboratory Science, College of Health Science, Debre Markos University, Debre Markos, Ethiopia
| | - Tebelay Dilnessa
- Department of Medical Laboratory Science, College of Health Science, Debre Markos University, Debre Markos, Ethiopia
| | - Tengchuan Jin
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of innate immunity and chronic disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Science, Shanghai, China
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