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Khan A, Bealy MA, Alharbi B, Khan S, Alharethi SH, Al-Soud WA, Mohammad T, Hassan MI, Alshammari N, Ahmed Al-Keridis L. Discovering potential inhibitors of Raf proto-oncogene serine/threonine kinase 1: a virtual screening approach towards anticancer drug development. J Biomol Struct Dyn 2024; 42:1846-1857. [PMID: 37104027 DOI: 10.1080/07391102.2023.2204380] [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: 02/17/2023] [Accepted: 04/08/2023] [Indexed: 04/28/2023]
Abstract
Raf proto-oncogene serine/threonine kinase 1 (RAF1 or c-Raf) is a serine/threonine protein kinase crucial in regulating cell growth, differentiation, and survival. Any disruption or overexpression of RAF1 can result in neoplastic transformation and other disorders such as cardiomyopathy, Noonan syndrome, leopard syndrome, etc. RAF1 has been identified as a potential therapeutic target in drug development against various complex diseases, including cancer, due to its remarkable role in disease progression. Here, we carried out a multitier virtual screening study involving different in-silico approaches to discover potential inhibitors of RAF1. After applying the Lipinski rule of five, we retrieved all phytocompounds from the IMPPAT database based on their physicochemical properties. We performed a molecular docking-based virtual screening and got top hits with the best binding affinity and ligand efficiency. Then we screened out the selected hits using the PAINS filter, ADMET properties, and other druglike features. Eventually, PASS evaluation identifies two phytocompounds, Moracin C and Tectochrysin, with appreciable anti-cancerous properties. Finally, all-atom molecular dynamics simulation (MDS) followed by interaction analysis was performed on the elucidated compounds in complex with RAF1 for 200 ns to investigate their time-evolution dynamics and interaction mechanism. Molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) and Dynamical Cross-Correlation Matrix (DCCM) analyses then followed these results from the simulated trajectories. According to the results, the elucidated compounds stabilize the RAF1 structure and lead to fewer conformational alterations. The results of the current study indicated that Moracin C and Tectochrysin could serve as potential inhibitors of RAF1 after required validation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Afsha Khan
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
| | - Mohamed Ahmed Bealy
- Department of Pathology, College of Medicine, University of Ha'il, Hail, Saudi Arabia
| | - Bandar Alharbi
- Department of Medical Laboratory Science, College of Applied Medical Sciences, University of Ha'il, Hail, Saudi Arabia
| | - Shama Khan
- Faculty of Health Science, South Africa Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Salem Hussain Alharethi
- Department of Biological Science, College of Arts and Science, Najran University, Najran, Saudi Arabia
| | - Waleed Abu Al-Soud
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Jouf University, Sakaka, Saudi Arabia
| | - Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Nawaf Alshammari
- Department of Biology, College of Science, University of Ha'il, Ha'il, Saudi Arabia
| | - Lamya Ahmed Al-Keridis
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
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Hassan MI, Anjum D, Mohammad T, Alam M, Khan MS, Shahwan M, Shamsi A, Yadav DK. Integrated virtual screening and MD simulation study to discover potential inhibitors of Lyn-kinase: targeting cancer therapy. J Biomol Struct Dyn 2023; 41:10558-10568. [PMID: 36495308 DOI: 10.1080/07391102.2022.2154849] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 11/28/2022] [Indexed: 12/14/2022]
Abstract
Tyrosine-protein kinase Lyn (LynK) has emerged as one of the most attractive therapeutic targets for cancer and diabetes. In this study, we used a multistep virtual screening process of natural compounds to discover potential inhibitors of LynK from the IMPPAT database. The primary filters were based on Lipinski rules, ADMET properties, and PAINS patterns. Then, binding affinities and interaction analyses were carried out for the high-affinity selectivity of the compounds towards LynK. Eventually, two natural compounds, Glabrene and Lactupicrin, were identified with high affinity and specificity for the LynK-binding pocket. Both compounds exhibited drug-like properties, as predicted by ADMET analysis and physicochemical parameters. The molecular dynamics (MD) simulation study revealed that these compounds bind to the ATP-binding pocket of LynK and interact with functionally significant residues with stability without inducing any significant structural changes to the protein. Ultimately, the identified compounds may be regarded as promising LynK inhibitors and can be used as lead molecules in the drug development against LynK-related diseases.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Darakshan Anjum
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
| | - Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Manzar Alam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Mohd Shahnawaz Khan
- Department of Biochemistry, College of Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Moyad Shahwan
- Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates
| | - Anas Shamsi
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
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Jiang H, Zhou S, Li G. Novel biomarkers used for early diagnosis and tyrosine kinase inhibitors as targeted therapies in colorectal cancer. Front Pharmacol 2023; 14:1189799. [PMID: 37719843 PMCID: PMC10502318 DOI: 10.3389/fphar.2023.1189799] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 08/14/2023] [Indexed: 09/19/2023] Open
Abstract
Colorectal cancer (CRC) is the third most common and second most lethal type of cancer worldwide, presenting major health risks as well as economic costs to both people and society. CRC survival chances are significantly higher if the cancer is diagnosed and treated early. With the development of molecular biology, numerous initiatives have been undertaken to identify novel biomarkers for the early diagnosis of CRC. Pathological disorders can be diagnosed at a lower cost with the help of biomarkers, which can be detected in stool, blood, and tissue samples. Several lines of evidence suggest that the gut microbiota could be used as a biomarker for CRC screening and treatment. CRC treatment choices include surgical resection, chemotherapy, immunotherapy, gene therapy, and combination therapies. Targeted therapies are a relatively new and promising modality of treatment that has been shown to increase patients' overall survival (OS) rates and can inhibit cancer cell development. Several small-molecule tyrosine kinase inhibitors (TKIs) are being investigated as potential treatments due to our increasing awareness of CRC's molecular causes and oncogenic signaling. These compounds may inhibit critical enzymes in controlling signaling pathways, which are crucial for CRC cells' development, differentiation, proliferation, and survival. On the other hand, only one of the approximately 42 TKIs that demonstrated anti-tumor effects in pre-clinical studies has been licensed for clinical usage in CRC. A significant knowledge gap exists when bringing these tailored medicines into the clinic. As a result, the emphasis of this review is placed on recently discovered biomarkers for early diagnosis as well as tyrosine kinase inhibitors as possible therapy options for CRC.
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Xia B, Zheng L, Li Y, Sun W, Liu Y, Li L, Pang J, Chen J, Li J, Cheng H. The brief overview, antivirus and anti-SARS-CoV-2 activity, quantitative methods, and pharmacokinetics of cepharanthine: a potential small-molecule drug against COVID-19. Front Pharmacol 2023; 14:1098972. [PMID: 37583901 PMCID: PMC10423819 DOI: 10.3389/fphar.2023.1098972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 07/11/2023] [Indexed: 08/17/2023] Open
Abstract
To effectively respond to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), an increasing number of researchers are focusing on the antiviral activity of cepharanthine (CEP), which is a clinically approved drug being used for over 70 years. This review aims to provide a brief overview of CEP and summarize its recent findings in quantitative analysis, pharmacokinetics, therapeutic potential, and mechanism in antiviral and anti-SARS-CoV-2 activity. Given its remarkable capacity against SARS-CoV-2 infection in vitro and in vivo, with its primary target organ being the lungs, and its good pharmacokinetic profile; mature and stable manufacturing technique; and its advantages of safety, effectiveness, and accessibility, CEP has become a promising drug candidate for treating COVID-19 despite being an old drug.
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Affiliation(s)
- Binbin Xia
- Department of Pharmacy, Beijing Luhe Hospital Affiliated to Capital Medical University, Beijing, China
| | - Li Zheng
- Department of Pharmacy, China Aerospace Science & Industry Corporation 731 Hospital, Beijing, China
| | - Yali Li
- Department of Pharmacy, Beijing Luhe Hospital Affiliated to Capital Medical University, Beijing, China
| | - Wenfang Sun
- Department of Pharmacy, Beijing Luhe Hospital Affiliated to Capital Medical University, Beijing, China
| | - Yang Liu
- Department of Pharmacy, Beijing Luhe Hospital Affiliated to Capital Medical University, Beijing, China
| | - Liushui Li
- Department of Pharmacy, Beijing Luhe Hospital Affiliated to Capital Medical University, Beijing, China
| | - Jingyao Pang
- Department of Pharmacy, Beijing Luhe Hospital Affiliated to Capital Medical University, Beijing, China
| | - Jing Chen
- Department of Pharmacy, Beijing Luhe Hospital Affiliated to Capital Medical University, Beijing, China
| | - Jiaxin Li
- Department of Pharmacy, Beijing Hospital, National Center of Gerontology, Beijing, China
| | - Hua Cheng
- Department of Pharmacy, Beijing Luhe Hospital Affiliated to Capital Medical University, Beijing, China
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Cui H, Yang J, Yang B, Hao Y, Shi X, Zhang D, Yang X, Zhang T, Zhao D, Yuan X, Chen X, Liu X, Zheng H, Zhang K. Cyproheptadine hydrochloride inhibits African swine fever viral replication in vitro. Microb Pathog 2023; 175:105957. [PMID: 36572196 DOI: 10.1016/j.micpath.2022.105957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 09/16/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022]
Abstract
African swine fever (ASF) is an infectious disease caused by the African swine fever virus (ASFV), and has a high mortality rate. It has caused serious socioeconomic consequences worldwide. Currently, there are no available commercial vaccines or antiviral drug interventions. D1133L is one of the key genes for ASFV replication and antiviral drug screening. In this study, a virtual screening software program, PyRx, was used to screen libraries of compounds against the potential drug target D1133L. Twelve compounds with a high affinity for ASFV D1133L were screened, and cyproheptadine hydrochloride (periactin) was identified as a candidate drug. The periactin has little cytotoxicity, and which dose-dependently inhibited ASFV replication in vitro. Further research indicated that periactin could significantly down-regulate D1133L at the transcriptional and protein levels with RT-qPCR and western blot methods. This study has provided important candidate drugs for the prevention and treatment of ASF, as well as biological materials and new fields of view for the research and development of vaccines and drugs for ASFV.
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Affiliation(s)
- Huimei Cui
- State Key Laboratory of Veterinary Etiological Biology, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730000, PR China
| | - Jinke Yang
- State Key Laboratory of Veterinary Etiological Biology, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730000, PR China
| | - Bo Yang
- State Key Laboratory of Veterinary Etiological Biology, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730000, PR China
| | - Yu Hao
- State Key Laboratory of Veterinary Etiological Biology, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730000, PR China
| | - Xijuan Shi
- State Key Laboratory of Veterinary Etiological Biology, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730000, PR China
| | - Dajun Zhang
- State Key Laboratory of Veterinary Etiological Biology, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730000, PR China
| | - Xing Yang
- State Key Laboratory of Veterinary Etiological Biology, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730000, PR China
| | - Ting Zhang
- State Key Laboratory of Veterinary Etiological Biology, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730000, PR China
| | - DengShuai Zhao
- State Key Laboratory of Veterinary Etiological Biology, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730000, PR China
| | - Xingguo Yuan
- State Key Laboratory of Veterinary Etiological Biology, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730000, PR China
| | - Xuehui Chen
- State Key Laboratory of Veterinary Etiological Biology, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730000, PR China
| | - Xiangtao Liu
- State Key Laboratory of Veterinary Etiological Biology, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730000, PR China
| | - Haixue Zheng
- State Key Laboratory of Veterinary Etiological Biology, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730000, PR China.
| | - Keshan Zhang
- State Key Laboratory of Veterinary Etiological Biology, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730000, PR China.
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