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Du J, Li J, Wen J, Liu J, Xiao H, Zhang A, Yang D, Sun P, Zhou H, Xu J. A Systematic Hierarchical Virtual Screening Model for RhlR Inhibitors Based on PCA, Pharmacophore, Docking, and Molecular Dynamics. Int J Mol Sci 2024; 25:8000. [PMID: 39063243 PMCID: PMC11276863 DOI: 10.3390/ijms25148000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 07/16/2024] [Accepted: 07/18/2024] [Indexed: 07/28/2024] Open
Abstract
RhlR plays a key role in the quorum sensing of Pseudomonas aeruginosa. The current structure-activity relationship (SAR) studies of RhlR inhibitors mainly focus on elucidating the functional groups. Based on a systematic review of previous research on RhlR inhibitors, this study aims to establish a systematic, hierarchical screening model for RhlR inhibitors. We initially established a database and utilized principal component analysis (PCA) to categorize the inhibitors into two classes. Based on the training set, pharmacophore models were established to elucidate the structural characteristics of ligands. Subsequently, molecular docking, molecular dynamics simulations, and the calculation of binding free energy and strain energy were performed to validate the crucial interactions between ligands and receptors. Then, the screening criteria for RhlR inhibitors were established hierarchically based on ligand structure characteristics, ligand-receptor interaction, and receptor affinity. Test sets were finally employed to validate the hierarchical virtual screening model by comparing it with the current SAR studies of RhlR inhibitors. The hierarchical screening model was confirmed to possess higher accuracy and a true positive rate, which holds promise for subsequent screening and the discovery of active RhlR inhibitors.
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Affiliation(s)
- Jiarui Du
- College of Pharmacy, Jinan University, Guangzhou 511436, China; (J.D.); (J.L.); (J.W.); (J.L.); (H.X.); (A.Z.); (D.Y.); (P.S.)
| | - Jiahao Li
- College of Pharmacy, Jinan University, Guangzhou 511436, China; (J.D.); (J.L.); (J.W.); (J.L.); (H.X.); (A.Z.); (D.Y.); (P.S.)
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou 510632, China
| | - Juqi Wen
- College of Pharmacy, Jinan University, Guangzhou 511436, China; (J.D.); (J.L.); (J.W.); (J.L.); (H.X.); (A.Z.); (D.Y.); (P.S.)
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou 510632, China
| | - Jun Liu
- College of Pharmacy, Jinan University, Guangzhou 511436, China; (J.D.); (J.L.); (J.W.); (J.L.); (H.X.); (A.Z.); (D.Y.); (P.S.)
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou 510632, China
| | - Haichuan Xiao
- College of Pharmacy, Jinan University, Guangzhou 511436, China; (J.D.); (J.L.); (J.W.); (J.L.); (H.X.); (A.Z.); (D.Y.); (P.S.)
| | - Antian Zhang
- College of Pharmacy, Jinan University, Guangzhou 511436, China; (J.D.); (J.L.); (J.W.); (J.L.); (H.X.); (A.Z.); (D.Y.); (P.S.)
| | - Dongdong Yang
- College of Pharmacy, Jinan University, Guangzhou 511436, China; (J.D.); (J.L.); (J.W.); (J.L.); (H.X.); (A.Z.); (D.Y.); (P.S.)
| | - Pinghua Sun
- College of Pharmacy, Jinan University, Guangzhou 511436, China; (J.D.); (J.L.); (J.W.); (J.L.); (H.X.); (A.Z.); (D.Y.); (P.S.)
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou 510632, China
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization, Ministry of Education, School of Pharmacy, Shihezi University, Shihezi 832003, China
| | - Haibo Zhou
- College of Pharmacy, Jinan University, Guangzhou 511436, China; (J.D.); (J.L.); (J.W.); (J.L.); (H.X.); (A.Z.); (D.Y.); (P.S.)
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou 510632, China
| | - Jun Xu
- College of Pharmacy, Jinan University, Guangzhou 511436, China; (J.D.); (J.L.); (J.W.); (J.L.); (H.X.); (A.Z.); (D.Y.); (P.S.)
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou 510632, China
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Alharbi B, Alharethi SH, Al-Soud WA, Ahmed Al-Keridis L, Aljohani AA, Jairajpuri DS, Alshammari N, Adnan M. Exploring the potential of phytochemicals as inhibitors of 3'-phosphoadenosine 5'-phosphosulfate synthase 1 targeting cancer therapy. J Biomol Struct Dyn 2024; 42:3193-3203. [PMID: 37184152 DOI: 10.1080/07391102.2023.2212810] [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: 05/03/2023] [Indexed: 05/16/2023]
Abstract
3'-phosphoadenosine 5'-phosphosulfate synthase 1 (PAPSS1) is an enzyme that critically synthesises the biologically active form of sulfate (PAPS) for all sulfation reactions. The discovery of PAPSS1 as a possible drug target for cancer therapy, specifically in non-small cell lung cancer, has prompted us to investigate potential small-molecule inhibitors of PAPSS1. Here, a structure-based virtual screening method was used to search for phytochemicals in the IMPPAT database to find potential inhibitors of PAPSS1. The primary hits were selected based on their physicochemical, ADMET, and drug-like properties. Then, the binding affinities were calculated and analyzed the interactions to identify safer and more effective hits. The research identified two phytochemicals, Guggulsterone and Corylin, that exhibited significant affinity and specific interaction with the ATP-binding pocket of PAPSS1. Structural observations made by molecular docking were further accompanied by molecular dynamics (MD) simulations and principal component analysis (PCA) to examine the conformational changes and stability of PAPSS1 with the elucidated compounds Guggulsterone and Corylin. MD simulation results suggested that the binding of Guggulsterone and Corylin stabilizes the PAPSS1 structure, leading to fewer conformational changes. This implies that these compounds may be useful in developing PAPSS1 inhibitors for the therapeutic development against non-small cell lung cancer (NSCLC). This study highlights the potential of phytochemicals as PAPSS1 inhibitors and the utility of computational approaches in drug discovery.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Bandar Alharbi
- Department of Medical Laboratory Science, College of Applied Medical Sciences, University of Ha'il, Ha'il, Saudi Arabia
| | - 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
| | - Lamya Ahmed Al-Keridis
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Abdullah A Aljohani
- Department of Clinical laboratory Science, College of Applied Medical Sciences-Qurayyat, Jouf University, Sakaka, Saudi Arabia
| | - Deeba Shamim Jairajpuri
- Department of Medical Biochemistry, College of Medicine and Medical Sciences, Arabian Gulf University, Manama, Bahrain
| | - Nawaf Alshammari
- Department of Biology, College of Science, University of Ha'il, Ha'il, Saudi Arabia
| | - Mohd Adnan
- Department of Biology, College of Science, University of Ha'il, Ha'il, Saudi Arabia
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Bhattacharya S, Sadhukhan D, Saraswathy R. Role of sex in immune response and epigenetic mechanisms. Epigenetics Chromatin 2024; 17:1. [PMID: 38247002 PMCID: PMC10802034 DOI: 10.1186/s13072-024-00525-x] [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: 11/01/2023] [Accepted: 01/05/2024] [Indexed: 01/23/2024] Open
Abstract
The functioning of the human immune system is highly dependent on the sex of the individual, which comes by virtue of sex chromosomes and hormonal differences. Epigenetic mechanisms such as X chromosome inactivation, mosaicism, skewing, and dimorphism in X chromosome genes and Y chromosome regulatory genes create a sex-based variance in the immune response between males and females. This leads to differential susceptibility in immune-related disorders like infections, autoimmunity, and malignancies. Various naturally available immunomodulators are also available which target immune pathways containing X chromosome genes.
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Affiliation(s)
- Sombodhi Bhattacharya
- Biomedical Genetics Research Lab, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, 632014, India
| | - Debasmita Sadhukhan
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, 632014, India
| | - Radha Saraswathy
- Biomedical Genetics Research Lab, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, 632014, India.
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, 632014, India.
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Shahwan M, Anwar S, Yadav DK, Khan MS, Shamsi A. Experimental and Computational Insights into the Molecular Interactions between Human Transferrin and Apigenin: Implications of Natural Compounds in Targeting Neuroinflammation. ACS OMEGA 2023; 8:46967-46976. [PMID: 38107922 PMCID: PMC10719914 DOI: 10.1021/acsomega.3c06799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/18/2023] [Accepted: 10/30/2023] [Indexed: 12/19/2023]
Abstract
Neuroinflammation plays a vital role in Alzheimer's disease (AD) pathogenesis and other neurodegenerative disorders (NDs). Presently, only symptomatic treatments are available and no disease-modifying drugs are available for AD and other NDs. Thus, targeting AD-associated neuroinflammation with anti-inflammatory compounds and antioxidants has recently been given much focus. Now, flavonoids are being increasingly investigated as therapeutic agents to treat inflammation; apigenin has a neuroprotective effect. Iron dyshomeostasis plays a key role in sustaining the neuroinflammatory phenotype, highlighting the importance of maintaining iron balance, in which human transferrin (HTF) plays a vital role in this aspect. Herein, we explored the binding and dynamics of the HTF-apigenin complex using multifaceted computational and experimental approaches. Molecular docking revealed that apigenin occupies the iron-binding pocket of HTF, forming hydrogen bonds with critical residues Arg475 and Thr686. Molecular dynamics simulations deciphered a dynamic view of the HTF-apigenin complex's behavior (300 ns) and suggested that the complex maintained a relatively stable conformation. The results of spectroscopic observations delineated significant binding of apigenin with HTF and stable HTF-apigenin complex formation. The observed binding mechanism and conformational stability could pave the way for developing novel therapeutic strategies to target neuroinflammation by apigenin in the context of iron homeostasis.
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Affiliation(s)
- Moyad Shahwan
- Center
for Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman 346, United Arab
Emirates
| | - Saleha Anwar
- Centre
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Dharmendra Kumar Yadav
- College
of Pharmacy, Gachon University of Medicine
and Science, Incheon 21565, Republic
of Korea
| | - Mohd Shahnawaz Khan
- Department
of Biochemistry, College of Science, King
Saud University, Riyadh 11451, Saudi Arabia
| | - Anas Shamsi
- Center
for Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman 346, United Arab
Emirates
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Alrouji M, Alhumaydhi FA, Al Abdulmonem W, Sharaf SE, Shahwan M, Majarisi T, Atiya A, Shamsi A. Identifying β-secretase 1 (BACE1) inhibitors from plant-based compounds: an approach targeting Alzheimer's therapeutics employing molecular docking and dynamics simulation. Mol Divers 2023:10.1007/s11030-023-10726-3. [PMID: 37728805 DOI: 10.1007/s11030-023-10726-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 08/28/2023] [Indexed: 09/21/2023]
Abstract
β-secretase 1 (BACE1) is an enzyme that is involved in generating beta-amyloid peptides and is believed to have a significant role in the development of Alzheimer's disease (AD). Therefore, BACE1 has gained attention as a potential therapeutic target for treating AD. Modern drug discovery studies are being conducted to identify potential inhibitors of BACE1, with the goal of reducing the production of beta-amyloid peptides and, thus, slowing the progression of AD. Here, we used a multistep virtual screening methodology to identify phytoconstituents from the IMPPAT library that could inhibit the activity of BACE1. Molecular docking was employed to select initial hits based on their binding affinity toward BACE1. Screening for PAINS patterns, ADMET and PASS properties, was then used to identify potential molecules for BACE1 inhibition. In the end, we discovered two natural compounds, Peiminine and 27-Deoxywithaferin A, which demonstrated a strong affinity, effectiveness, and specific interactions for the BACE1-active site. The elucidated molecules also displayed drug likeliness. A 200 ns molecular dynamics (MD) simulation was conducted to investigate the interaction mechanism, complex stability, and conformational dynamics of BACE1 with Peiminine and 27-Deoxywithaferin A. The MD simulations demonstrated that BACE1 was stable during the simulation with Peiminine and 27-Deoxywithaferin A. Overall, the results suggested that Peiminine and 27-Deoxywithaferin A hold significant potential as scaffolds in drug development efforts targeting BACE1 for the purpose of treating AD.
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Affiliation(s)
- Mohammed Alrouji
- Department of Medical Laboratories, College of Applied Medical Sciences, Shaqra University, 11961, Shaqra, Saudi Arabia
| | - Fahad A Alhumaydhi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, 52571, Buraydah, Saudi Arabia
| | - Waleed Al Abdulmonem
- Department of Pathology, College of Medicine, Qassim University, P.O. Box 6655, 51452, Buraydah, Saudi Arabia
| | - Sharaf E Sharaf
- Pharmaceutical Chemistry Department, College of Pharmacy, Umm Al-Qura University, Mecca, Saudi Arabia
| | - Moyad Shahwan
- Centre of Medical and Bio-allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates
| | - Taghreed Majarisi
- Department of Pharmacognosy, College of Pharmacy, King Khalid University (KKU), Guraiger St., 62529, Abha, Saudi Arabia
| | - Akhtar Atiya
- Department of Pharmacognosy, College of Pharmacy, King Khalid University (KKU), Guraiger St., 62529, Abha, Saudi Arabia.
| | - Anas Shamsi
- Centre of Medical and Bio-allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates.
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Alam M, Ahmed S, Abid M, Hasan GM, Islam A, Hassan MI. Therapeutic targeting of microtubule affinity-regulating kinase 4 in cancer and neurodegenerative diseases. J Cell Biochem 2023; 124:1223-1240. [PMID: 37661636 DOI: 10.1002/jcb.30468] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/12/2023] [Accepted: 08/21/2023] [Indexed: 09/05/2023]
Abstract
Microtubule affinity-regulating kinase 4 (MARK4) is a member of the Ser/Thr protein kinase family, phosphorylates the microtubule-connected proteins and plays a vital role in causing cancers and neurodegenerative diseases. This kinase modulates multiple signaling pathways, including mammalian target of rapamycin, nuclear factor-κB, and Hippo-signaling, presumably responsible for cancer and Alzheimer's. MARK4 acts as a negative controller of the Hippo-kinase cassette for promoting YAP/TAZ action, and the loss of MARK4 detains the tumorigenic properties of cancer cells. MARK4 is involved in tau hyperphosphorylation that consequently affects neurodegeneration. MARK4 is a promising drug target for cancer, diabetes, and Alzheimer's. Developing the potent and selective inhibitors of MAKR4 are promising in the therapeutic management of associated diseases. Despite its great significance, a few reviews are available to discuss its structure, function and clinical significance. In the current review, we aimed to provide detailed information on the structural features of MARK4 targeted in drug development and its role in various signaling pathways related to cancer and neurodegenerative diseases. We further described the therapeutic potential of MARK4 inhibitors in preventing numerous diseases. Finally, the updated information on MARK4 will be helpful in the further development of effective therapeutic molecules.
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Affiliation(s)
- Manzar Alam
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Sarfraz Ahmed
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
- Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Mohammad Abid
- Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Gulam Mustafa Hasan
- Department of Biochemistry, College of Medicine, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Asimul Islam
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Md Imtaiyaz Hassan
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
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Hasan G, Hassan MI, Sohal SS, Shamsi A, Alam M. Therapeutic Targeting of Regulated Signaling Pathways of Non-Small Cell Lung Carcinoma. ACS OMEGA 2023; 8:26685-26698. [PMID: 37546685 PMCID: PMC10398694 DOI: 10.1021/acsomega.3c02424] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 06/15/2023] [Indexed: 08/08/2023]
Abstract
Non-small cell lung carcinoma (NSCLC) is the most common cancer globally. Phytochemicals and small molecule inhibitors significantly prevent varying types of cancers, including NSCLC. These therapeutic molecules serve as important sources for new drugs that interfere with cellular proliferation, apoptosis, metastasis, and angiogenesis by regulating signaling pathways. These molecules affect several cellular signaling cascades, including p53, NF-κB, STAT3, RAS, MAPK/ERK, Wnt, and AKT/PI3K, and are thus implicated in the therapeutic management of cancers. This review aims to describe the bioactive compounds and small-molecule inhibitors, their anticancer action, and targeting cellular signaling cascades in NSCLC. We highlighted the therapeutic potential of Epigallocatechin gallate (EGCG), Perifosine, ABT-737, Thymoquinine, Quercetin, Venetoclax, Gefitinib, and Genistein. These compounds are implicated in the therapeutic management of NSCLC. This review further offers deeper mechanistic insights into different signaling pathways that could be targeted for NSCLC therapy by phytochemicals and small-molecule inhibitors.
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Affiliation(s)
- Gulam
Mustafa Hasan
- Department
of Biochemistry, College of Medicine, Prince
Sattam Bin Abdulaziz University, P.O. Box 173, Al-Kharj 11942, Saudi Arabia
| | - Md. Imtaiyaz Hassan
- Centre
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Sukhwinder Singh Sohal
- Respiratory
Translational Research Group, Department of Laboratory Medicine, School
of Health Sciences, College of Health and Medicine, University of Tasmania, Launceston 7001, Tasmania, Australia
| | - Anas Shamsi
- Centre
of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman 346, United Arab
Emirates
| | - Manzar Alam
- Centre
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
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