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Lenin B, Ramasubramanyan S, Vetrivel U, Chitipothu S. Virtual screening and multilevel precision-based prioritisation of natural inhibitors targeting the ATPase domain of human DNA topoisomerase II alpha. J Biomol Struct Dyn 2023; 41:15177-15195. [PMID: 36898858 DOI: 10.1080/07391102.2023.2187234] [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: 11/15/2022] [Accepted: 02/25/2023] [Indexed: 03/12/2023]
Abstract
Human DNA topoisomerase II alpha (hTopIIα) is a classic chemotherapeutic drug target. The existing hTopIIα poisons cause numerous side effects such as the development of cardiotoxicity, secondary malignancies, and multidrug resistance. The use of catalytic inhibitors targeting the ATP-binding cavity of the enzyme is considered a safer alternative due to the less deleterious mechanism of action. Hence, in this study, we carried out high throughput structure-based virtual screening of the NPASS natural product database against the ATPase domain of hTopIIα and identified the five best ligand hits. This was followed by comprehensive validation through molecular dynamics simulations, binding free energy calculation and ADMET analysis. On stringent multilevel prioritization, we identified promising natural product catalytic inhibitors that showed high binding affinity and stability within the ligand-binding cavity and may serve as ideal hits for anticancer drug development.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Barathi Lenin
- Centre for Bioinformatics, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Chennai, Tamil Nadu, India
| | - Sharada Ramasubramanyan
- RS Mehta Jain Department of Biochemistry and Cell Biology, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Chennai, Tamil Nadu, India
| | - Umashankar Vetrivel
- Centre for Bioinformatics, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Chennai, Tamil Nadu, India
- National Institute of Traditional Medicine, Indian Council of Medical Research, Belagavi, Karnataka, India
| | - Srujana Chitipothu
- Centre for Bioinformatics, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Chennai, Tamil Nadu, India
- Central Research Instrumentation Facility, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Chennai, Tamil Nadu, India
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Al-Kuraishy HM, Al-Gareeb AI, Hetta HF, Alexiou A, Papadakis M, Batiha GES. Heparanase is the possible link between monkeypox and Covid-19: robust candidature in the mystic and present perspective. AMB Express 2023; 13:13. [PMID: 36705773 PMCID: PMC9880376 DOI: 10.1186/s13568-023-01517-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 01/18/2023] [Indexed: 01/28/2023] Open
Abstract
Heparanase (HPSE) is an endoglycosidase cleaves heparan sulfate (HS) and this contributes to the degradation and remodeling of the extracellular matrix. HS cleaved by HPSE induces activation of autophagy and formation of autophagosommes which facilitate binding of HPSE to the HS and subsequent release of growth factors. The interaction between HPSE and HS triggers releases of chemokines and cytokines which affect inflammatory response and cell signaling pathways with development of hyperinflammation, cytokine storm (CS) and coagulopathy. HPSE expression is induced by both SARS-CoV-2 and monkeypox virus (MPXV) leading to induction release of pro-inflammatory cytokines, endothelial dysfunction and thrombotic events. Co-infection of MPX with SARS-CoV-2 may occur as we facing many outbreaks of MPX cases during Covid-19 pandemic. Therefore, targeting of HPSE by specific inhibitors may reduce the risk of complications in both SARS-CoV-2 and MPXV infections. Taken together, HPSE could be a potential link between MPX with SARS-CoV-2 in Covid-19 era.
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Affiliation(s)
- Hayder M. Al-Kuraishy
- Department of Clinical Pharmacology and Therapeutic Medicine, College of Medicine, ALmustansiriyiah University, Baghdad, Iraq
| | - Ali I. Al-Gareeb
- Department of Clinical Pharmacology and Therapeutic Medicine, College of Medicine, ALmustansiriyiah University, Baghdad, Iraq
| | - Helal F. Hetta
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Assiut University, Assiut, 71515 Egypt
| | - Athanasios Alexiou
- Department of Science and Engineering, Novel Global Community Educational Foundation, Hebersham, NSW 2770 Australia
- AFNP Med, 1030 Vienna, Austria
| | - Marios Papadakis
- Department of Surgery II, University Hospital Witten-Herdecke, University of Witten-Herdecke, Heusnerstrasse 40, 42283 Wuppertal, Germany
| | - Gaber El-Saber Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicine, Damanhour University, AlBeheira, Damanhour, 22511 Egypt
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Øvestad IT, Engesæter B, Halle MK, Akbari S, Bicskei B, Lapin M, Austdal M, Janssen EAM, Krakstad C, Lillesand M, Nordhus M, Munk AC, Gudlaugsson EG. High-Grade Cervical Intraepithelial Neoplasia (CIN) Associates with Increased Proliferation and Attenuated Immune Signaling. Int J Mol Sci 2021; 23:ijms23010373. [PMID: 35008799 PMCID: PMC8745058 DOI: 10.3390/ijms23010373] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 12/27/2021] [Indexed: 01/10/2023] Open
Abstract
Implementation of high-risk human papilloma virus (HPV) screening and the increasing proportion of HPV vaccinated women in the screening program will reduce the percentage of HPV positive women with oncogenic potential. In search of more specific markers to identify women with high risk of cancer development, we used RNA sequencing to compare the transcriptomic immune-profile of 13 lesions with cervical intraepithelial neoplasia grade 3 (CIN3) or adenocarcinoma in situ (AIS) and 14 normal biopsies from women with detected HPV infections. In CIN3/AIS lesions as compared to normal tissue, 27 differential expressed genes were identified. Transcriptomic analysis revealed significantly higher expression of a number of genes related to proliferation, (CDKN2A, MELK, CDK1, MKI67, CCNB2, BUB1, FOXM1, CDKN3), but significantly lower expression of genes related to a favorable immune response (NCAM1, ARG1, CD160, IL18, CX3CL1). Compared to the RNA sequencing results, good correlation was achieved with relative quantitative PCR analysis for NCAM1 and CDKN2A. Quantification of NCAM1 positive cells with immunohistochemistry showed epithelial reduction of NCAM1 in CIN3/AIS lesions. In conclusion, NCAM1 and CDKN2A are two promising candidates to distinguish whether women are at high risk of developing cervical cancer and in need of frequent follow-up.
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Affiliation(s)
- Irene Tveiterås Øvestad
- Department of Pathology, Stavanger University Hospital, 4011 Stavanger, Norway; (S.A.); (B.B.); (E.A.M.J.); (M.L.); (M.N.); (E.G.G.)
- Correspondence: ; Tel.: +47-9093-2314
| | - Birgit Engesæter
- Section for Cervical Cancer Screening, Cancer Registry of Norway, 0304 Oslo, Norway;
| | - Mari Kyllesø Halle
- Department of Obstetrics and Gynaecology, Haukeland University Hospital, 5053 Bergen, Norway; (M.K.H.); (C.K.)
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, 5053 Bergen, Norway
| | - Saleha Akbari
- Department of Pathology, Stavanger University Hospital, 4011 Stavanger, Norway; (S.A.); (B.B.); (E.A.M.J.); (M.L.); (M.N.); (E.G.G.)
| | - Beatrix Bicskei
- Department of Pathology, Stavanger University Hospital, 4011 Stavanger, Norway; (S.A.); (B.B.); (E.A.M.J.); (M.L.); (M.N.); (E.G.G.)
| | - Morten Lapin
- Department of Haematology and Oncology, Stavanger University Hospital, 4011 Stavanger, Norway;
| | - Marie Austdal
- Section of Biostatistics, Department of Research, Stavanger University Hospital, 4011 Stavanger, Norway;
| | - Emiel A. M. Janssen
- Department of Pathology, Stavanger University Hospital, 4011 Stavanger, Norway; (S.A.); (B.B.); (E.A.M.J.); (M.L.); (M.N.); (E.G.G.)
- Department of Chemistry, Bioscience and Environmental Technology, University of Stavanger, 4036 Stavanger, Norway
| | - Camilla Krakstad
- Department of Obstetrics and Gynaecology, Haukeland University Hospital, 5053 Bergen, Norway; (M.K.H.); (C.K.)
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, 5053 Bergen, Norway
| | - Melinda Lillesand
- Department of Pathology, Stavanger University Hospital, 4011 Stavanger, Norway; (S.A.); (B.B.); (E.A.M.J.); (M.L.); (M.N.); (E.G.G.)
| | - Marit Nordhus
- Department of Pathology, Stavanger University Hospital, 4011 Stavanger, Norway; (S.A.); (B.B.); (E.A.M.J.); (M.L.); (M.N.); (E.G.G.)
| | - Ane Cecilie Munk
- Department of Gynaecology, Sørlandet Hospital, 4604 Kristiansand, Norway;
| | - Einar G. Gudlaugsson
- Department of Pathology, Stavanger University Hospital, 4011 Stavanger, Norway; (S.A.); (B.B.); (E.A.M.J.); (M.L.); (M.N.); (E.G.G.)
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Wang H, Zheng Y, Sun Q, Zhang Z, Zhao M, Peng C, Shi S. Ginsenosides emerging as both bifunctional drugs and nanocarriers for enhanced antitumor therapies. J Nanobiotechnology 2021; 19:322. [PMID: 34654430 PMCID: PMC8518152 DOI: 10.1186/s12951-021-01062-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 09/28/2021] [Indexed: 12/12/2022] Open
Abstract
Ginsenosides, the main components isolated from Panax ginseng, can play a therapeutic role by inducing tumor cell apoptosis and reducing proliferation, invasion, metastasis; by enhancing immune regulation; and by reversing tumor cell multidrug resistance. However, clinical applications have been limited because of ginsenosides' physical and chemical properties such as low solubility and poor stability, as well as their short half-life, easy elimination, degradation, and other pharmacokinetic properties in vivo. In recent years, developing a ginsenoside delivery system for bifunctional drugs or carriers has attracted much attention from researchers. To create a precise treatment strategy for cancer, a variety of nano delivery systems and preparation technologies based on ginsenosides have been conducted (e.g., polymer nanoparticles [NPs], liposomes, micelles, microemulsions, protein NPs, metals and inorganic NPs, biomimetic NPs). It is desirable to design a targeted delivery system to achieve antitumor efficacy that can not only cross various barriers but also can enhance immune regulation, eventually converting to a clinical application. Therefore, this review focused on the latest research about delivery systems encapsulated or modified with ginsenosides, and unification of medicines and excipients based on ginsenosides for improving drug bioavailability and targeting ability. In addition, challenges and new treatment methods were discussed to support the development of these new tumor therapeutic agents for use in clinical treatment.
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Affiliation(s)
- Hong Wang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Yu Zheng
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Qiang Sun
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Zhen Zhang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Mengnan Zhao
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Cheng Peng
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
| | - Sanjun Shi
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
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Thummadi NB, T M, Vindal V, P M. Prioritizing the candidate genes related to cervical cancer using the moment of inertia tensor. Proteins 2021; 90:363-371. [PMID: 34468998 DOI: 10.1002/prot.26226] [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: 06/14/2021] [Revised: 08/07/2021] [Accepted: 08/16/2021] [Indexed: 12/24/2022]
Abstract
It is well known that cervical cancer poses the fourth most malignancy threat to women worldwide among all cancer types. There is a tremendous improvement in realizing the underlying molecular associations in cervical cancer. Several studies reported pieces of evidence for the involvement of various genes in the disease progression. However, with the ever-evolving bioinformatics tools, there has been an upsurge in predicting numerous genes responsible for cervical cancer progression and making it highly complex to target the genes for further evaluation. In this article, we prioritized the candidate genes based on the sequence similarity analysis with known cancer genes. For this purpose, we used the concept of the moment of inertia tensor, which reveals the similarities between the protein sequences more efficiently. Tensor for moment of inertia explores the similarity of the protein sequences based on the physicochemical properties of amino acids. From our analysis, we obtained 14 candidate cervical cancer genes, which are highly similar to known cervical cancer genes. Further, we analyzed the GO terms and prioritized these genes based on the number of hits with biological process, molecular functions, and their involvement in KEGG pathways. We also discussed the evidence-based involvement of the prioritized genes in other cancers and listed the available drugs for those genes.
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Affiliation(s)
- Neelesh Babu Thummadi
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, India
| | - Mallikarjuna T
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, India
| | - Vaibhav Vindal
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, India
| | - Manimaran P
- School of Physics, University of Hyderabad, Gachibowli, Hyderabad, India
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