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Xu QX, Guo L, Li Y, Wang ZW, Hu P, Yang GM, Pan Y. In silico screening-based discovery of benzamide derivatives as inhibitors of Rho-associated kinase-1 (ROCK1). J Biomol Struct Dyn 2024; 42:7467-7484. [PMID: 37668086 DOI: 10.1080/07391102.2023.2253918] [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: 02/09/2023] [Accepted: 07/17/2023] [Indexed: 09/06/2023]
Abstract
As a pivotal node in modulating various cell behaviors, Rho-associated kinase-1 (ROCK1) has attracted significant attention as a promising therapeutic target in a variety of diseases. Benzamide has been widely reported as a ROCK1 inhibitors in recent years. To better understand its pharmacological properties and to explore its potential inhibitors, a series of ROCK1 inhibitors derived from N-methyl-4-(4-pyrazolidinyl) benzamides (MPBs) were investigated by using three-dimensional quantitative structure-activity relationship (3D-QSAR) models, pharmacophore models, molecular docking, and molecular dynamics (MD) simulation. The comparative Molecular Field Analysis (CoMFA) model (q2 = 0.616, R2 = 0.972, ONC = 4, and r2pred = 0.983) and the best Comparative Molecular Similarity Indices Analysis (CoMSIA) model (q2= 0.740, R2 = 0.982, ONC = 6, and r2pred = 0.824) exhibited reliable predictability with satisfactory validation parameters. In the subsequent virtual screening, VS03 and VS05 were identified to have superior predicted activities and higher docking scores, meanwhile they demonstrated to be reasonably stable in the binding pocket through MD simulations. These results provide a significant theoretical direction for the rational design and development of novel ROCK1 inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Qi-Xuan Xu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Liang Guo
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yuan Li
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Zhao-Wei Wang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Po Hu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Guang-Ming Yang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yang Pan
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
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Putra SSS, Chew CY, Hayyan A, Elgharbawy AAM, Taskin-Tok T, Hayyan M, Ngoh GC, Saleh J, Al Abdulmonem W, Alghsham RS, Nor MRM, Aldaihani AGH, Basirun WJ. Nanodiamonds and natural deep eutectic solvents as potential carriers for lipase. Int J Biol Macromol 2024; 270:132245. [PMID: 38729477 DOI: 10.1016/j.ijbiomac.2024.132245] [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: 01/09/2024] [Revised: 04/04/2024] [Accepted: 05/07/2024] [Indexed: 05/12/2024]
Abstract
This study investigates the use of nanodiamonds (ND) as a promising carrier for enzyme immobilization and compares the effectiveness of immobilized and native enzymes. Three different enzyme types were tested, of which Rhizopus niveus lipase (RNL) exhibited the highest relative activity, up to 350 %. Under optimized conditions (1 h, pH 7.0, 40 °C), the immobilized ND-RNL showed a maximum specific activity of 0.765 U mg-1, significantly higher than native RNL (0.505 U mg-1). This study highlights a notable enhancement in immobilized lipase; furthermore, the enzyme can be recycled in the presence of a natural deep eutectic solvent (NADES), retaining 76 % of its initial activity. This aids in preserving the native conformation of the protein throughout the reusability process. A test on brine shrimp revealed that even at low concentrations, ND-RNL had minimal toxicity, indicating its low cytotoxicity. The in silico molecular dynamics simulations performed in this study offer valuable insights into the mechanism of interactions between RNL and ND, demonstrating that RNL immobilization onto NDs enhances its efficiency and stability. All told, these findings highlight the immense potential of ND-immobilized RNL as an excellent candidate for biological applications and showcase the promise of further research in this field.
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Affiliation(s)
| | - Chia Yong Chew
- Department of Chemical Engineering, Faculty of Engineering, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Adeeb Hayyan
- Department of Chemical Engineering, Faculty of Engineering, Universiti Malaya, Kuala Lumpur 50603, Malaysia; Sustainable Process Engineering Centre (SPEC), Faculty of Engineering, Universiti Malaya, Kuala Lumpur 50603, Malaysia.
| | - Amal A M Elgharbawy
- International Institute for Halal Research and Training (INHART), International Islamic University Malaysia, Kuala Lumpur 50728, Malaysia; Bioenvironmental Engineering Research Centre (BERC), Department of Biotechnology Engineering, Faculty of Engineering, International Islamic University Malaysia (IIUM), 53100 Kuala Lumpur, Malaysia.
| | - Tugba Taskin-Tok
- Gaziantep University, Faculty of Arts and Sciences, Department of Chemistry, Gaziantep, Turkey; Gaziantep University, Institute of Health Sciences, Department of Bioinformatics and Computational Biology, Gaziantep, Turkey
| | - Maan Hayyan
- Chemical Engineering Program, Faculty of Engineering & Technology, Muscat University, PO Box 550, Muscat P.C.130, Sultanate of Oman.
| | - Gek Cheng Ngoh
- Department of Chemical Engineering, Faculty of Engineering, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Jehad Saleh
- Chemical Engineering Department, King Saud University, P.O. Box 800, Riyadh 11421, Saudi Arabia
| | - Waleed Al Abdulmonem
- Department of Pathology, College of Medicine, Qassim University, Buraydah 51452, Saudi Arabia
| | - Ruqaih S Alghsham
- Department of Pathology, College of Medicine, Qassim University, Buraydah 51452, Saudi Arabia
| | - Mohd Roslan Mohd Nor
- Halal Research Group, Academy of Islamic Studies, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | | | - Wan Jefrey Basirun
- Department of Chemistry, Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia
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You Y, Zhu K, Wang J, Liang Q, Li W, Wang L, Guo B, Zhou J, Feng X, Shi J. ROCK inhibitor: Focus on recent updates. CHINESE CHEM LETT 2023. [DOI: 10.1016/j.cclet.2023.108336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
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Behera S, Behera A, Mekap SK, Behera CC, Kadam A, Mohanty PK. Periplaneta americana L . a potential source of traditional medicine: chemometric analysis, in vitro and in silico study. J Biomol Struct Dyn 2022; 40:9931-9947. [PMID: 34151747 DOI: 10.1080/07391102.2021.1938681] [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: 12/16/2022]
Abstract
'Mayurbhanj is the ethnic dominant tribal population district in Odisha, India. The triabl's of Mayurbhanj depends on traditional medicines since time immemorial for health-related issues. Due to the imperative ethnic claim of traditional healers, the financial stringency of the patient community and the necessity to produce a better therapeutic effect has led to investigate ethno zoological sources and to find out the biochemical moiety responsible for the healing process. Considering the ethnic communities' acceptability of the zoological source as traditional medicine, the current evidence-based research study is conducted to investigate the biochemical moiety present in Periplaneta americana, responsible for therapeutic activity. The whole powdered Periplaneta americana was extracted using maceration techniques with n-hexane and methanol as solvent. The obtained extracts were subjected to GC-MS analysis to identify the biochemical moiety. To check the potential biological activity, an in-vitro antimicrobial test was carried out in both turbidimetry and a viable count method against E. coli. Moreover, the obtained biochemical molecules were exposed to in silico studies for their binding modes and their affinity using Discovery studio software. The major compounds were found to be hexadecanoic acid, methyl ester, n-hexadecanoic acid, oleic acid, octadecanoic acid along with other minor constituents. The maximum inhibitory activity of n-hexane and methanol extract against S. aureus at a concentration of 400 µg/mL was found to be 89 and 87%, respectively. The binding models of almost all identified compounds confer very good binding affinities with some key and strong non-covalent interactions with various amino acid residues of receptor active site pocket, which predict the compounds to be potent inhibitors of various infectious bacteria. These findings suggested that the hexane extract of P. americana could be exploited as a potential natural source. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Suchismeeta Behera
- Postgraduate Department of Zoology, Utkal University, Bhubaneswar, India.,State Forensic Science Laboratory, Bhubaneswar, India
| | - Amulyaratna Behera
- School of Pharmacy and Life Sciences, Centurion University of Technology and Management, Bhubaneswar, India
| | - Suman Kumar Mekap
- School of Pharmacy and Life Sciences, Centurion University of Technology and Management, Bhubaneswar, India
| | - Chinmaya Chidananda Behera
- School of Pharmacy and Life Sciences, Centurion University of Technology and Management, Bhubaneswar, India
| | - Atul Kadam
- Department of Pharmaceutics, Shree Santkrupa College of Pharmacy, Ghogaon, India
| | - Prafulla K Mohanty
- Postgraduate Department of Zoology, Utkal University, Bhubaneswar, India
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Investigating the Anticancer Activity of G-Rh1 Using In Silico and In Vitro Studies (A549 Lung Cancer Cells). MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238311. [PMID: 36500403 PMCID: PMC9890317 DOI: 10.3390/molecules27238311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/11/2022] [Accepted: 11/16/2022] [Indexed: 11/30/2022]
Abstract
Ginsenoside Rh1 (G-Rh1), a possible bioactive substance isolated from the Korean Panax ginseng Meyer, has a wide range of pharmacological effects. In this study, we have investigated the anticancer efficacy of G-Rh1 via in silico and in vitro methodologies. This study mainly focuses on the two metastatic regulators, Rho-associated protein kinase 1 (ROCK1) and RhoA, along with other standard apoptosis regulators. The ROCK1 protein is a member of the active serine/threonine kinase family that is crucial for many biological processes, including cell division, differentiation, and death, as well as many cellular processes and muscle contraction. The abnormal activation of ROCK1 kinase causes several disorders, whereas numerous studies have also shown that RhoA is expressed highly in various cancers, including colon, lung, ovarian, gastric, and liver malignancies. Hence, inhibiting both ROCK1 and RhoA will be promising in preventing metastasis. Therefore, the molecular level interaction of G-Rh1 with the ROCK1 and RhoA active site residues from the preliminary screening clearly shows its inhibitory potential. Molecular dynamics simulation and principal component analysis give essential insights for comprehending the conformational changes that result from G-Rh1 binding to ROCK1 and RhoA. Further, MTT assay was employed to examine the potential cytotoxicity in vitro against human lung cancer cells (A549) and Raw 264.7 Murine macrophage cells. Thus, G-Rh1 showed significant cytotoxicity against human lung adenocarcinoma (A549) at 100 µg/mL. In addition, we observed an elevated level of reactive oxygen species (ROS) generation, perhaps promoting cancer cell toxicity. Additionally, G-Rh1 suppressed the mRNA expression of RhoA, ROCK1, MMP1, and MMP9 in cancer cell. Accordingly, G-Rh1 upregulated the p53, Bax, Caspase 3, caspase 9 while Bcl2 is downregulated intrinsic pathway. The findings from our study propose that the anticancer activity of G-Rh1 may be related to the induction of apoptosis by the RhoA/ROCK1 signaling pathway. As a result, this study evaluated the functional drug-like compound G-Rh1 from Panax ginseng in preventing and treating lung cancer adenocarcinoma via regulating metastasis and apoptosis.
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Lee DH, Lee JY, Hong DY, Lee EC, Park SW, Jo YN, Park YJ, Cho JY, Cho YJ, Chae SH, Lee MR, Oh JS. ROCK and PDE-5 Inhibitors for the Treatment of Dementia: Literature Review and Meta-Analysis. Biomedicines 2022; 10:biomedicines10061348. [PMID: 35740369 PMCID: PMC9219677 DOI: 10.3390/biomedicines10061348] [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: 05/06/2022] [Revised: 06/02/2022] [Accepted: 06/05/2022] [Indexed: 12/14/2022] Open
Abstract
Dementia is a disease in which memory, thought, and behavior-related disorders progress gradually due to brain damage caused by injury or disease. It is mainly caused by Alzheimer’s disease or vascular dementia and several other risk factors, including genetic factors. It is difficult to treat as its incidence continues to increase worldwide. Many studies have been performed concerning the treatment of this condition. Rho-associated kinase (ROCK) and phosphodiesterase-5 (PDE-5) are attracting attention as pharmacological treatments to improve the symptoms. This review discusses how ROCK and PDE-5 affect Alzheimer’s disease, vascular restructuring, and exacerbation of neuroinflammation, and how their inhibition helps improve cognitive function. In addition, the results of the animal behavior analysis experiments utilizing the Morris water maze were compared through meta-analysis to analyze the effects of ROCK inhibitors and PDE-5 inhibitors on cognitive function. According to the selection criteria, 997 publications on ROCK and 1772 publications on PDE-5 were screened, and conclusions were drawn through meta-analysis. Both inhibitors showed good improvement in cognitive function tests, and what is expected of the synergy effect of the two drugs was confirmed in this review.
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Affiliation(s)
- Dong-Hun Lee
- Department of Neurosurgery, College of Medicine, Soonchunhyang University, Cheonan Hospital, Cheonan 31151, Korea; (D.-H.L.); (J.Y.L.); (D.-Y.H.); (E.C.L.); (S.-W.P.)
- Soonchunhyang Institute of Medi-bio Science (SIMS), Soon Chun Hyang University, Cheonan 31151, Korea
| | - Ji Young Lee
- Department of Neurosurgery, College of Medicine, Soonchunhyang University, Cheonan Hospital, Cheonan 31151, Korea; (D.-H.L.); (J.Y.L.); (D.-Y.H.); (E.C.L.); (S.-W.P.)
| | - Dong-Yong Hong
- Department of Neurosurgery, College of Medicine, Soonchunhyang University, Cheonan Hospital, Cheonan 31151, Korea; (D.-H.L.); (J.Y.L.); (D.-Y.H.); (E.C.L.); (S.-W.P.)
- Soonchunhyang Institute of Medi-bio Science (SIMS), Soon Chun Hyang University, Cheonan 31151, Korea
| | - Eun Chae Lee
- Department of Neurosurgery, College of Medicine, Soonchunhyang University, Cheonan Hospital, Cheonan 31151, Korea; (D.-H.L.); (J.Y.L.); (D.-Y.H.); (E.C.L.); (S.-W.P.)
- Soonchunhyang Institute of Medi-bio Science (SIMS), Soon Chun Hyang University, Cheonan 31151, Korea
| | - Sang-Won Park
- Department of Neurosurgery, College of Medicine, Soonchunhyang University, Cheonan Hospital, Cheonan 31151, Korea; (D.-H.L.); (J.Y.L.); (D.-Y.H.); (E.C.L.); (S.-W.P.)
- Soonchunhyang Institute of Medi-bio Science (SIMS), Soon Chun Hyang University, Cheonan 31151, Korea
| | - Yu Na Jo
- Department of Medicine, College of Medicine, Soonchunhyang University, Cheonan 31151, Korea; (Y.N.J.); (Y.J.P.); (J.Y.C.); (Y.J.C.); (S.H.C.)
| | - Yu Jin Park
- Department of Medicine, College of Medicine, Soonchunhyang University, Cheonan 31151, Korea; (Y.N.J.); (Y.J.P.); (J.Y.C.); (Y.J.C.); (S.H.C.)
| | - Jae Young Cho
- Department of Medicine, College of Medicine, Soonchunhyang University, Cheonan 31151, Korea; (Y.N.J.); (Y.J.P.); (J.Y.C.); (Y.J.C.); (S.H.C.)
| | - Yoo Jin Cho
- Department of Medicine, College of Medicine, Soonchunhyang University, Cheonan 31151, Korea; (Y.N.J.); (Y.J.P.); (J.Y.C.); (Y.J.C.); (S.H.C.)
| | - Su Hyun Chae
- Department of Medicine, College of Medicine, Soonchunhyang University, Cheonan 31151, Korea; (Y.N.J.); (Y.J.P.); (J.Y.C.); (Y.J.C.); (S.H.C.)
| | - Man Ryul Lee
- Soonchunhyang Institute of Medi-bio Science (SIMS), Soon Chun Hyang University, Cheonan 31151, Korea
- Correspondence: (M.R.L.); (J.S.O.)
| | - Jae Sang Oh
- Department of Neurosurgery, College of Medicine, Soonchunhyang University, Cheonan Hospital, Cheonan 31151, Korea; (D.-H.L.); (J.Y.L.); (D.-Y.H.); (E.C.L.); (S.-W.P.)
- Soonchunhyang Institute of Medi-bio Science (SIMS), Soon Chun Hyang University, Cheonan 31151, Korea
- Correspondence: (M.R.L.); (J.S.O.)
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Cai R, Wang Y, Huang Z, Zou Q, Pu Y, Yu C, Cai Z. Role of RhoA/ROCK signaling in Alzheimer's disease. Behav Brain Res 2021; 414:113481. [PMID: 34302876 DOI: 10.1016/j.bbr.2021.113481] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/22/2021] [Accepted: 07/17/2021] [Indexed: 12/11/2022]
Abstract
Rho-associated coiled-coil kinase (ROCK), a serine/threonine kinase regulated by the small GTPase RhoA, is involved in regulating cell migration, proliferation, and survival. Numerous studies have shown that the RhoA/ROCK signaling pathway can promote Alzheimer's disease (AD) occurrence. ROCK activation increases β-secretase activity and promotes amyloid-beta (Aβ) production; moreover, Aβ further activates ROCK. This is suggestive of a possible positive feedback role for Aβ and ROCK. Moreover, ROCK activation promotes the formation of neurofibrillary tangles and abnormal synaptic contraction. Additionally, ROCK activation can promote the neuroinflammatory response by activating microglia and astrocytes to release inflammatory cytokines. Therefore, ROCK is a promising drug target in AD; further, there is a need to elucidate the specific mechanism of action.
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Affiliation(s)
- RuoLan Cai
- Zunyi Medical University, Zunyi, 563003, China; Department of Neurology, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, China; Chongqing Key Laboratory of Neurodegenerative Diseases, Chongqing, 400013, China; Department of Neurology, Chongqing General Hospital, University of Chinese Academy of Sciences, Chongqing, 400013, China
| | - YangYang Wang
- Chongqing Key Laboratory of Neurodegenerative Diseases, Chongqing, 400013, China; Department of Neurology, Chongqing General Hospital, University of Chinese Academy of Sciences, Chongqing, 400013, China
| | - ZhenTing Huang
- Chongqing Key Laboratory of Neurodegenerative Diseases, Chongqing, 400013, China; Department of Neurology, Chongqing General Hospital, University of Chinese Academy of Sciences, Chongqing, 400013, China
| | - Qian Zou
- Chongqing Key Laboratory of Neurodegenerative Diseases, Chongqing, 400013, China; Department of Neurology, Chongqing General Hospital, University of Chinese Academy of Sciences, Chongqing, 400013, China
| | - YinShuang Pu
- Chongqing Key Laboratory of Neurodegenerative Diseases, Chongqing, 400013, China; Department of Neurology, Chongqing General Hospital, University of Chinese Academy of Sciences, Chongqing, 400013, China
| | - Changyin Yu
- Department of Neurology, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, China.
| | - Zhiyou Cai
- Chongqing Key Laboratory of Neurodegenerative Diseases, Chongqing, 400013, China; Department of Neurology, Chongqing General Hospital, University of Chinese Academy of Sciences, Chongqing, 400013, China.
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Tatar G, Salmanli M, Dogru Y, Tuzuner T. Evaluation of the effects of chlorhexidine and several flavonoids as antiviral purposes on SARS-CoV-2 main protease: molecular docking, molecular dynamics simulation studies. J Biomol Struct Dyn 2021; 40:7656-7665. [PMID: 33749547 DOI: 10.1080/07391102.2021.1900919] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The recent outbreak of COVID-19 caused by a new human coronavirus called SARS-CoV-2, is continually causing worldwide human infections and deaths.The main protease (3CLpro), which plays a critical role in the life cycle of the virus, makes it an attractive target for the development of antiviral agents effective against coronaviruses (CoVs).Currently, there is no specific viral protein targeted therapeutics.Therefore, there is a need to investigate an alternative therapy which will prevent the spread of the infection, by focusing on the transmission of the virus.Chlorhexidine (CHX) and flavonoids agents have shown that they have a viral inactivation effect against enveloped viruses, and thus facilitate the struggle against oral transmission.Especially, some flavonoids have very strong antiviral activity in SARS-CoV and MERS-CoV main protease.This study was conducted to evaluate the CHX and flavonoids compounds potential antiviral effects on SARS-CoV-2 main protease through virtual screening for the COVID-19 treatment by molecular docking method.According to the results of this study, CHX, Kaempferol-3-rutinoside, Rutin, Quercetin 3-beta-D-glucoside and Isobavachalcone exhibited the best binding affinity against this enzyme, and also these compounds showed significant inhibitory effects compared to the SARS-CoV-2 main protease crystal structure inhibitor (N3).Especially, these compounds mainly interact with His41, Cys145, His163, Met165, Glu166 and Thr190 in SARS-CoV-2 main protease binding site. Further, MD simulation analysis also confirmed that stability of these interactions between the enzyme and these five compounds.The current study provides to guide clinical trials for broad-spectrum CHX and bioactive flavonoids to reduce the viral load of the infection and possibly disease progression.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Gizem Tatar
- Faculty of Medicine, Department of Biostatistics and Medical Informatics, Karadeniz Technical University, Trabzon, Turkey
| | - Merve Salmanli
- Dentistry Faculty of Dentistry, Department of Pediatric, Karadeniz Technical University, Trabzon, Turkey
| | - Yakup Dogru
- Dentistry Faculty of Dentistry, Department of Pediatric, Karadeniz Technical University, Trabzon, Turkey
| | - Tamer Tuzuner
- Dentistry Faculty of Dentistry, Department of Pediatric, Karadeniz Technical University, Trabzon, Turkey
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Tang ZQ, Zhao L, Chen GX, Chen CYC. Novel and versatile artificial intelligence algorithms for investigating possible GHSR1α and DRD1 agonists for Alzheimer's disease. RSC Adv 2021; 11:6423-6446. [PMID: 35423219 PMCID: PMC8694922 DOI: 10.1039/d0ra10077c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 01/18/2021] [Indexed: 11/21/2022] Open
Abstract
Hippocampal lesions are recognized as the earliest pathological changes in Alzheimer's disease (AD). Recent researches have shown that the co-activation of growth hormone secretagogue receptor 1α (GHSR1α) and dopamine receptor D1 (DRD1) could recover the function of hippocampal synaptic and cognition. We combined traditional virtual screening technology with artificial intelligence models to screen multi-target agonists for target proteins from TCM database and a novel boost Generalized Regression Neural Network (GRNN) model was proposed in this article to improve the poor adjustability of GRNN. R-square was chosen to evaluate the accuracy of these artificial intelligent models. For the GHSR1α agonist dataset, Adaptive Boosting (AdaBoost), Linear Ridge Regression (LRR), Support Vector Machine (SVM), and boost GRNN achieved good results; the R-square of the test set of these models reached 0.900, 0.813, 0.708, and 0.802, respectively. For the DRD1 agonist dataset, Gradient Boosting (GB), Random Forest (RF), SVM, and boost GRNN achieved good results; the R-square of the test set of these models reached 0.839, 0.781, 0.763, and 0.815, respectively. According to these values of R-square, it is obvious that boost GRNN and SVM have better adaptability for different data sets and boost GRNN is more accurate than SVM. To evaluate the reliability of screening results, molecular dynamics (MD) simulation experiments were performed to make sure that candidates were docked well in the protein binding site. By analyzing the results of these artificial intelligent models and MD experiments, we suggest that 2007_17103 and 2007_13380 are the possible dual-target drugs for Alzheimer's disease (AD).
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Affiliation(s)
- Zi-Qiang Tang
- Artificial Intelligence Medical Center, School of Intelligent Systems Engineering, Sun Yat-sen University Shenzhen Guangzhou 510275 China
| | - Lu Zhao
- Artificial Intelligence Medical Center, School of Intelligent Systems Engineering, Sun Yat-sen University Shenzhen Guangzhou 510275 China
- Department of Clinical Laboratory, The Sixth Affiliated Hospital, Sun Yat-sen University Guangzhou 510655 China
| | - Guan-Xing Chen
- Artificial Intelligence Medical Center, School of Intelligent Systems Engineering, Sun Yat-sen University Shenzhen Guangzhou 510275 China
| | - Calvin Yu-Chian Chen
- Artificial Intelligence Medical Center, School of Intelligent Systems Engineering, Sun Yat-sen University Shenzhen Guangzhou 510275 China
- Department of Medical Research, China Medical University Hospital Taichung 40447 Taiwan
- Department of Bioinformatics and Medical Engineering, Asia University Taichung 41354 Taiwan
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Gu Z, Yan T, Yan F. Rational design and improvement of the dimerization-disrupting peptide selectivity between ROCK-I and ROCK-II kinase isoforms in cerebrovascular diseases. J Mol Recognit 2020; 33:e2835. [PMID: 31995258 DOI: 10.1002/jmr.2835] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/17/2019] [Accepted: 12/25/2019] [Indexed: 02/05/2023]
Abstract
Human rho-associated coiled-coil forming kinases (ROCKs) ROCK-I and ROCK-II have been documented as attractive therapeutic targets for cerebrovascular diseases. Although ROCK-I and ROCK-II share a high degree of structural conservation and are both present in classic rho/ROCK signaling pathway, their downstream substrates and pathological functions may be quite different. Selective targeting of the two kinase isoforms with traditional small-molecule inhibitors is a great challenge due to their surprisingly high homology in kinase domain (~90%) and the full identity in kinase active site (100%). Here, instead of developing small-molecule drugs to selectively target the adenosine triphosphate (ATP) site of two isoforms, we attempt to design peptide agents to selectively disrupt the homo-dimerization event of ROCK kinases through their dimerization domains which have a relatively low conservation (~60%). Three helical peptides H1, H2, and H3 are split from the kinase dimerization domain, from which the isolated H2 peptide is found to have the best capability to rebind at the dimerization interface. A simulated annealing (SA) iteration method is used to improve the H2 peptide selectivity between ROCK-I and ROCK-II. The method accepts moderate degradation in peptide affinity in order to maximize the affinity difference between peptide binding to the two isoforms. Consequently, hundreds of parallel SA runs yielded six promising peptide candidates with ROCK-I over ROCK-II (I over II [IoII]) calculated selectivity and four promising peptide candidates with ROCK-II over ROCK-I (II over I [IIoI]) calculated selectivity. Subsequent anisotropy assays confirm that the selectivity values range between 13.2-fold and 83.9-fold for IoII peptides, and between 5.8-fold and 21.2-fold for IIoI peptides, which are considerably increased relative to wild-type H2 peptide (2.6-fold for IoII and 2.0-fold for IIoI). The molecular origin of the designed peptide selectivity is also analyzed at structural level; it is revealed that the peptide residues can be classified into conserved, non-conserved, and others, in which the non-conserved residues play a crucial role in defining peptide selectivity, while conserved residues confer stability to kinase-peptide binding.
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Affiliation(s)
- Zhengtian Gu
- Department of Neurology, Affiliated Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
| | - Tingting Yan
- Department of Pediatrics, Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, China
| | - Fuling Yan
- Department of Neurology, Affiliated Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
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Yalcin E, Erkmen C, Taskin-Tok T, Caglayan MG. Fluorescence chemosensing of meldonium using a cross-reactive sensor array. Analyst 2020; 145:3345-3352. [DOI: 10.1039/d0an00209g] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Differential sensing of meldonium was achieved using fluorescent chemosensors.
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Affiliation(s)
- Ergin Yalcin
- Iskenderun Technical University
- Faculty of Engineering and Natural Sciences
- Engineering Basic Sciences
- Hatay
- Turkey
| | - Cem Erkmen
- Ankara University
- Faculty of Pharmacy
- Department of Analytical Chemistry
- Ankara
- Turkey
| | - Tugba Taskin-Tok
- Gaziantep University
- Faculty of Arts and Sciences
- Department of Chemistry
- Gaziantep
- Turkey
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12
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Shahzad S, Karadurmus L, Dogan‐Topal B, Taskin‐Tok T, Shah A, Ozkan SA. Sensitive Nucleic Acid Detection at NH
2
‐MWCNTs Modified Glassy Carbon Electrode and its Application for Monitoring of Gemcitabine‐DNA Interaction. ELECTROANAL 2019. [DOI: 10.1002/elan.201900597] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Suniya Shahzad
- Ankara University Faculty of Pharmacy, Department of Analytical Chemistry 06100 Tandogan-Ankara Turkey
- Department of Chemistry Quaid-i-Azam University 45320 Islamabad Pakistan
| | - Leyla Karadurmus
- Ankara University Faculty of Pharmacy, Department of Analytical Chemistry 06100 Tandogan-Ankara Turkey
- AdıyamanUniversity Faculty of Pharmacy, Department of Analytical Chemistry Adıyaman Turkey
| | - Burcu Dogan‐Topal
- Ankara University Faculty of Pharmacy, Department of Analytical Chemistry 06100 Tandogan-Ankara Turkey
| | - Tugba Taskin‐Tok
- Gaziantep University Faculty of Arts and Science, Department of Chemistry +9027310 Gaziantep Turkey
- Gaziantep University Institute of Health Sciences, Department of Bioinformatics and Computational Biology 27310 Gaziantep Turkey
| | - Afzal Shah
- Department of Chemistry Quaid-i-Azam University 45320 Islamabad Pakistan
- Department of Chemistry, College of Science University of Bahrain Sakhir 32038 Bahrain
| | - Sibel A. Ozkan
- Ankara University Faculty of Pharmacy, Department of Analytical Chemistry 06100 Tandogan-Ankara Turkey
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13
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Arya H, Yadav CS, Lin SY, Syed SB, Charles MRC, Kannadasan S, Hsieh HP, Singh SS, Gajurel PR, Coumar MS. Design of a potent anticancer lead inspired by natural products from traditional Indian medicine. J Biomol Struct Dyn 2019; 38:3563-3577. [PMID: 31526250 DOI: 10.1080/07391102.2019.1664326] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Among the plant constituents of Clerodendrum colebrookianum Walp., acteoside, martinoside, and osmanthuside β6 interact with ROCK, a drug target for cancer. In this study, aglycone fragments of these plant constituents (caffeic acid, ferulic acid, and p-coumaric acid) along with the homopiperazine ring of fasudil (standard ROCK inhibitor) were used to design hybrid molecules. The designed molecules interact with the key hinge region residue Met156/Met157 of ROCK I/II in a stable manner according to our docking and molecular dynamics simulations. These compounds were synthesized and tested in vitro in SW480, MDA-MB-231, and A-549 cancer cell lines. The most promising compound was chemically optimized to obtain a thiourea analog, 6a (IC50 = 25 µM), which has >3-fold higher antiproliferative activity than fasudil (IC50 = 87 µM) in SW480 cells. Treatment with this molecule also inhibits the migration of colon cancer cells and induces cell apoptosis. Further, SPR experiments suggests that the binding affinity of 6a with ROCK I protein is better than that of fasudil. Hence, the drug-like natural product analog 6a constitutes a highly promising new anticancer lead.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hemant Arya
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Puducherry, India
| | - C Suresh Yadav
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Shu-Yu Lin
- Division of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Miaoli County, Taiwan R.O.C
| | - Safiulla Basha Syed
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Puducherry, India.,DBT- Interdisciplinary Program in Life Sciences, Pondicherry University, Kalapet, Puducherry, India
| | | | - Sathananthan Kannadasan
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Hsing-Pang Hsieh
- Division of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Miaoli County, Taiwan R.O.C
| | - Sorokhaibam Sureshkumar Singh
- Department of Forestry, North Eastern Regional Institute of Science and Technology (Deemed University), Nirjuli, India
| | - Padma Raj Gajurel
- Department of Forestry, North Eastern Regional Institute of Science and Technology (Deemed University), Nirjuli, India
| | - Mohane Selvaraj Coumar
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Puducherry, India
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14
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Dogan‐Topal B, Bakirhan NK, Tok TT, Ozkan SA. Electrochemical Determination and
in silico
Studies of Fludarabine on NH
2
Functionalized Multiwalled Carbon Nanotube Modified Glassy Carbon Electrode. ELECTROANAL 2019. [DOI: 10.1002/elan.201900347] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Burcu Dogan‐Topal
- Ankara University, Faculty of PharmacyDepartment of Analytical Chemistry, Tandogan Ankara Turkey
| | - Nurgul K. Bakirhan
- Hitit University, Faculty of Art&ScienceDepartment of Chemistry Corum Turkey
| | - Tugba Taskin Tok
- Gaziantep University, Faculty of Arts and SciencesDepartment of Chemistry Gaziantep Turkey
| | - Sibel A. Ozkan
- Ankara University, Faculty of PharmacyDepartment of Analytical Chemistry, Tandogan Ankara Turkey
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15
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Prakash O, Nath Dwivedi U. Identification of repurposed protein kinase B binders from FDA-approved drug library: a hybrid-structure activity relationship and systems modeling based approach. J Biomol Struct Dyn 2019; 38:660-672. [PMID: 30806166 DOI: 10.1080/07391102.2019.1585293] [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: 10/27/2022]
Abstract
Food and Drug Administration (FDA)-approved drugs may be repurposed against those diseases, for which their therapeutic action has not been described. The present study deals with repurposing FDA-approved drugs for selective targeting of protein kinase B (PKB/Akt) for anti-cancer activity, through a two-tier (Cell and Target) model hybridization protocol implemented with support vector machine-based learning method. The hybridization was done as per rules of reaction kinetics. The hybridization process was facilitated as a standalone application for free access at https://github.com/undwivedi/Akt-Selective.git. The selectivity of the ligands for PKB/Akt binding was also evaluated on the basis of mitophagy system model for anti-apoptotic activity. Screening of the FDA-approved drug library, using the developed H- SAR model, led to identification of four compounds (Cas nos. 94749-08-3, 57808-66-9, 62-13-5, 76-43-7), bearing the selectivity for PKB/Akt. Since, the identified compounds have already crossed the barriers of absorption, distribution, metabolism, excretion, toxicity in clinical trials, therefore are safe to be considered for repurposing individually or in combination with other drugs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Om Prakash
- Department of Biochemistry, Bioinformatics Infrastructure Facility, Centre of Excellence in Bioinformatics & Institute for Development of Advanced Computing, ONGC Centre for Advanced Studies University of Lucknow, Lucknow, Uttar Pradesh, India
| | - Upendra Nath Dwivedi
- Department of Biochemistry, Bioinformatics Infrastructure Facility, Centre of Excellence in Bioinformatics & Institute for Development of Advanced Computing, ONGC Centre for Advanced Studies University of Lucknow, Lucknow, Uttar Pradesh, India
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