1
|
Chua HM, Moshawih S, Kifli N, Goh HP, Ming LC. Insights into the computer-aided drug design and discovery based on anthraquinone scaffold for cancer treatment: A systematic review. PLoS One 2024; 19:e0301396. [PMID: 38776291 PMCID: PMC11111074 DOI: 10.1371/journal.pone.0301396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 03/14/2024] [Indexed: 05/24/2024] Open
Abstract
BACKGROUND In the search for better anticancer drugs, computer-aided drug design (CADD) techniques play an indispensable role in facilitating the lengthy and costly drug discovery process especially when natural products are involved. Anthraquinone is one of the most widely-recognized natural products with anticancer properties. This review aimed to systematically assess and synthesize evidence on the utilization of CADD techniques centered on the anthraquinone scaffold for cancer treatment. METHODS The conduct and reporting of this review were done in accordance to the Preferred Reporting Items for Systematic Reviews and Meta-analysis (PRISMA) 2020 guideline. The protocol was registered in the "International prospective register of systematic reviews" database (PROSPERO: CRD42023432904) and also published recently. The search strategy was designed based on the combination of concept 1 "CADD or virtual screening", concept 2 "anthraquinone" and concept 3 "cancer". The search was executed in PubMed, Scopus, Web of Science and MedRxiv on 30 June 2023. RESULTS Databases searching retrieved a total of 317 records. After deduplication and applying the eligibility criteria, the final review ended up with 32 articles in which 3 articles were found by citation searching. The CADD methods used in the studies were either structure-based alone (69%) or combined with ligand-based methods via parallel (9%) or sequential (22%) approaches. Molecular docking was performed in all studies, with Glide and AutoDock being the most popular commercial and public software used respectively. Protein data bank was used in most studies to retrieve the crystal structure of the targets of interest while the main ligand databases were PubChem and Zinc. The utilization of in-silico techniques has enabled a deeper dive into the structural, biological and pharmacological properties of anthraquinone derivatives, revealing their remarkable anticancer properties in an all-rounded fashion. CONCLUSION By harnessing the power of computational tools and leveraging the natural diversity of anthraquinone compounds, researchers can expedite the development of better drugs to address the unmet medical needs in cancer treatment by improving the treatment outcome for cancer patients.
Collapse
Affiliation(s)
- Hui Ming Chua
- PAP Rashidah Sa’adatul Bolkiah Institute of Health Sciences, Universiti Brunei Darussalam, Gadong, Brunei Darussalam
| | - Said Moshawih
- PAP Rashidah Sa’adatul Bolkiah Institute of Health Sciences, Universiti Brunei Darussalam, Gadong, Brunei Darussalam
| | - Nurolaini Kifli
- PAP Rashidah Sa’adatul Bolkiah Institute of Health Sciences, Universiti Brunei Darussalam, Gadong, Brunei Darussalam
| | - Hui Poh Goh
- PAP Rashidah Sa’adatul Bolkiah Institute of Health Sciences, Universiti Brunei Darussalam, Gadong, Brunei Darussalam
| | - Long Chiau Ming
- PAP Rashidah Sa’adatul Bolkiah Institute of Health Sciences, Universiti Brunei Darussalam, Gadong, Brunei Darussalam
- School of Medical and Life Sciences, Sunway University, Bandar Sunway, Malaysia
| |
Collapse
|
2
|
Chemical Composition and In Vitro and In Silico Antileishmanial Evaluation of the Essential Oil from Croton linearis Jacq. Stems. Antibiotics (Basel) 2022; 11:antibiotics11121712. [PMID: 36551370 PMCID: PMC9774621 DOI: 10.3390/antibiotics11121712] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022] Open
Abstract
Croton linearis Jacq. is an aromatic shrub that has been utilized in traditional medicine in the Bahamas, Jamaica, and Cuba. Recent studies have revealed the antiprotozoal potential of its leaves. The present work is aimed to identify the volatile constituents of essential oil from the stems of C. linearis (CLS-EO) and evaluate its in vitro antileishmanial activity. In addition, an in silico study of the molecular interactions was performed using molecular docking. A gas chromatographic-mass spectrometric analysis of CLS-EO identified 1,8-cineole (27.8%), α-pinene (11.1%), cis-sabinene (8.1%), p-cymene (5.7%), α-terpineol (4.4%), epi-γ-eudesmol (4.2%), linalool (3.9%), and terpinen-4-ol (2.6%) as major constituents. The evaluation of antileishmanial activity showed that CLS-EO has good activity on both parasite forms (IC50Promastigote = 21.4 ± 0.1 μg/mL; IC50Amastigote = 18.9 ± 0.3 μg/mL), with a CC50 of 49.0 ± 5.0 μg/mL on peritoneal macrophages from BALB/c mice (selectivity index = 2 and 3 using the promastigote and amastigote results). Molecular docking showed good binding of epi-γ-eudesmol with different target enzymes of Leishmania. This study is the first report of the chemical composition and anti-Leishmania evaluation of CLS-EO. These findings provide support for further studies of the antileishmanial effect of this product.
Collapse
|
3
|
Zolghadr L, Behbehani GR, PakBin B, Hosseini SA, Divsalar A, Gheibi N. Molecular dynamics simulations, molecular docking, and kinetics study of kaempferol interaction on Jack bean urease: Comparison of extended solvation model. Food Sci Nutr 2022; 10:3585-3597. [DOI: 10.1002/fsn3.2956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 04/30/2022] [Accepted: 05/25/2022] [Indexed: 11/11/2022] Open
Affiliation(s)
- Leila Zolghadr
- Department of Chemistry Faculty of Science Imam Khomeini International University Qazvin Iran
| | | | - Babak PakBin
- Department of Food Hygiene and Quality of Control Faculty of Veterinary Medicine University of Tehran Tehran Iran
- Medical Microbiology Research Center University of Medical sciences Qazvin Iran
| | - Seied Ali Hosseini
- Electrical Engineering Department Faculty of Engineering Imam Khomeini International University Qazvin Iran
| | - Adeleh Divsalar
- Department of Cell and Molecular Sciences Kharazmi University Tehran Iran
| | - Nematollah Gheibi
- Cellular and Molecular Research Center, Research Institute for Prevention of Non‐Communicable Diseases Qazvin University of Medical Sciences Qazvin Iran
| |
Collapse
|
4
|
Haider K, Rehman S, Pathak A, Najmi AK, Yar MS. Advances in 2-substituted benzothiazole scaffold-based chemotherapeutic agents. Arch Pharm (Weinheim) 2021; 354:e2100246. [PMID: 34467567 DOI: 10.1002/ardp.202100246] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 08/10/2021] [Accepted: 08/13/2021] [Indexed: 01/25/2023]
Abstract
Targeted therapy plays a pivotal role in cancer therapeutics by countering the drawbacks of conventional treatment like adverse events and drug resistance. Over the last decade, heterocyclic derivatives have received considerable attention as cytotoxic agents by modulating various signaling pathways. Benzothiazole is an important heterocyclic scaffold that has been explored for its therapeutic potential. Benzothiazole-based derivatives have emerged as potent inhibitors of enzymes such as EGFR, VEGFR, PI3K, topoisomerases, and thymidylate kinases. Several researchers have designed, synthesized, and evaluated benzothiazole scaffold-based enzyme inhibitors. Of these, several inhibitors have entered various phases of clinical trials. This review describes the recent advances and developments of benzothiazole architecture-based derivatives as potent anticancer agents.
Collapse
Affiliation(s)
- Kashif Haider
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research (SPER), Jamia Hamdard, New Delhi, India
| | - Sara Rehman
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research (SPER), Jamia Hamdard, New Delhi, India
| | - Ankita Pathak
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research (SPER), Jamia Hamdard, New Delhi, India
| | - Abul K Najmi
- Department of Pharmacology, School of Pharmaceutical Education and Research (SPER), Jamia Hamdard, New Delhi, India
| | - Mohammad S Yar
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research (SPER), Jamia Hamdard, New Delhi, India
| |
Collapse
|
5
|
Abstract
Molecular dynamics (MD) simulations have become increasingly useful in the modern drug development process. In this review, we give a broad overview of the current application possibilities of MD in drug discovery and pharmaceutical development. Starting from the target validation step of the drug development process, we give several examples of how MD studies can give important insights into the dynamics and function of identified drug targets such as sirtuins, RAS proteins, or intrinsically disordered proteins. The role of MD in antibody design is also reviewed. In the lead discovery and lead optimization phases, MD facilitates the evaluation of the binding energetics and kinetics of the ligand-receptor interactions, therefore guiding the choice of the best candidate molecules for further development. The importance of considering the biological lipid bilayer environment in the MD simulations of membrane proteins is also discussed, using G-protein coupled receptors and ion channels as well as the drug-metabolizing cytochrome P450 enzymes as relevant examples. Lastly, we discuss the emerging role of MD simulations in facilitating the pharmaceutical formulation development of drugs and candidate drugs. Specifically, we look at how MD can be used in studying the crystalline and amorphous solids, the stability of amorphous drug or drug-polymer formulations, and drug solubility. Moreover, since nanoparticle drug formulations are of great interest in the field of drug delivery research, different applications of nano-particle simulations are also briefly summarized using multiple recent studies as examples. In the future, the role of MD simulations in facilitating the drug development process is likely to grow substantially with the increasing computer power and advancements in the development of force fields and enhanced MD methodologies.
Collapse
|
6
|
Bansode P, Anantacharya R, Dhanavade M, Kamble S, Barale S, Sonawane K, Satyanarayan ND, Rashinkar G. Evaluation of drug candidature: In silico ADMET, binding interactions with CDK7 and normal cell line studies of potentially anti-breast cancer enamidines. Comput Biol Chem 2019; 83:107124. [PMID: 31563021 DOI: 10.1016/j.compbiolchem.2019.107124] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 09/02/2019] [Accepted: 09/10/2019] [Indexed: 12/20/2022]
Abstract
We have recently explored novel class of potentially anti-breast cancer active enamidines in which four molecules 4a-c and 4h showed higher anticancer activity compared to standard drug doxorubicin. As a part of extension of this work, we have further evaluated in silico cheminformatic studies on bioactivity prediction of synthesized series of enamidines using mole information. The normal cell line study of four lead compounds 4a-c and 4h against African green monkey kidney vero strain further revealed that the compounds complemented good selectivity in inhibition of cancer cells. The in silico bioactivity and molecular docking studies also revealed that the compounds have significant interactions with the drug targets. The results reveal that enamidine moieties are vital for anti-breast cancer activity as they possess excellent drug-like characteristics, being potentially good inhibitors of cyclin dependent kinases7 (CDK7).
Collapse
Affiliation(s)
- Prakash Bansode
- Department of Chemistry, Shivaji University, Kolhapur, 416004, M.S., India
| | - R Anantacharya
- Department of Pharmaceutical Chemistry, Kuvempu University, Post Graduate Centre, Kadur, 577548, Karnataka, India
| | - Maruti Dhanavade
- Department of Microbiology, Shivaji University, Kolhapur, 416004, M.S., India
| | - Subodh Kamble
- Department of Microbiology, Shivaji University, Kolhapur, 416004, M.S., India
| | - Sagar Barale
- Department of Microbiology, Shivaji University, Kolhapur, 416004, M.S., India
| | - Kailas Sonawane
- Department of Microbiology, Shivaji University, Kolhapur, 416004, M.S., India
| | - Nayak D Satyanarayan
- Department of Pharmaceutical Chemistry, Kuvempu University, Post Graduate Centre, Kadur, 577548, Karnataka, India
| | - Gajanan Rashinkar
- Department of Chemistry, Shivaji University, Kolhapur, 416004, M.S., India.
| |
Collapse
|
7
|
Puthumana SSE, Damodaran B. ICT‐Based Blue‐Emitting Dual‐Functional Probe (Ugi EML BLUE) for Bio‐Imaging and Cytotoxic Activities on HeLa Cells. ChemistrySelect 2019. [DOI: 10.1002/slct.201900474] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
| | - Bahulayan Damodaran
- Department of ChemistryUniversity of Calicut Malappuram 673635, Kerala India
| |
Collapse
|
8
|
Arba M, Nur-Hidayat A, Surantaadmaja SI, Tjahjono DH. Pharmacophore-based virtual screening for identifying β5 subunit inhibitor of 20S proteasome. Comput Biol Chem 2018; 77:64-71. [PMID: 30243108 DOI: 10.1016/j.compbiolchem.2018.08.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 08/16/2018] [Accepted: 08/26/2018] [Indexed: 12/13/2022]
Abstract
Proteasomal system plays an important role in maintaining cell homeostatis. Overexpression of proteasomes leads to several major diseases, such as cancer and autoimmune disorder. The β5 subunit of proteasome is a crucial active site in proteolysis, and targeting proteasome β5 subunit is essential for proteasome inhibition. In the present study, a pharmacophore-based virtual screening and molecular docking were employed to identify ligands as inhibitors of β5 subunit of proteasome. The pharmacophore features were built with one hydrogen bond donor, two hydrogen bond acceptors, and one hydrophobic feature using native ligand of proteasome (HU10), which was then used to screen ZINC database using ZINCPharmer. The retrieved virtual hits were subjected to molecular docking analysis using iDock. The best six hits were subjected to molecular dynamics (MD) simulation and each complex was stable during 40 ns MD simulation as indicated by root-mean-square-deviation (RMSD) and root-mean-square-fluctuation (RMSF) values. The current study identifies 5 best hits having better binding potentials than HU10 as predicted by molecular mechanics Poisson-Boltzmann Surface Area (MM-PBSA) method, i.e. Lig1540/ZINC33356240, Lig1546/ZINC33356235, Lig1522/ZINC20854878, Lig980/ZINC12391945, and Lig1119/ZINC19865241, which can be used in the development of new proteasome inhibitors.
Collapse
Affiliation(s)
- Muhammad Arba
- Faculty of Pharmacy, Halu Oleo University, Kendari, 93231, Indonesia.
| | - Andry Nur-Hidayat
- Faculty of Pharmacy, Halu Oleo University, Kendari, 93231, Indonesia
| | | | - Daryono H Tjahjono
- School of Pharmacy, Bandung Institute of Technology, Bandung, 40312, Indonesia
| |
Collapse
|
9
|
Molecular modeling on porphyrin derivatives as β5 subunit inhibitor of 20S proteasome. Comput Biol Chem 2018; 74:230-238. [DOI: 10.1016/j.compbiolchem.2018.03.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 02/08/2018] [Accepted: 03/05/2018] [Indexed: 12/28/2022]
|
10
|
Wang C, Greene D, Xiao L, Qi R, Luo R. Recent Developments and Applications of the MMPBSA Method. Front Mol Biosci 2018; 4:87. [PMID: 29367919 PMCID: PMC5768160 DOI: 10.3389/fmolb.2017.00087] [Citation(s) in RCA: 332] [Impact Index Per Article: 55.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 11/30/2017] [Indexed: 12/23/2022] Open
Abstract
The Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) approach has been widely applied as an efficient and reliable free energy simulation method to model molecular recognition, such as for protein-ligand binding interactions. In this review, we focus on recent developments and applications of the MMPBSA method. The methodology review covers solvation terms, the entropy term, extensions to membrane proteins and high-speed screening, and new automation toolkits. Recent applications in various important biomedical and chemical fields are also reviewed. We conclude with a few future directions aimed at making MMPBSA a more robust and efficient method.
Collapse
Affiliation(s)
- Changhao Wang
- Chemical and Materials Physics Graduate Program, University of California, Irvine, Irvine, CA, United States
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
- Department of Physics and Astronomy, University of California, Irvine, Irvine, CA, United States
| | - D'Artagnan Greene
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Li Xiao
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, United States
| | - Ruxi Qi
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Ray Luo
- Chemical and Materials Physics Graduate Program, University of California, Irvine, Irvine, CA, United States
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, United States
- Department of Chemical Engineering and Materials Science, University of California, Irvine, Irvine, CA, United States
| |
Collapse
|
11
|
Keretsu S, Balasubramanian PK, Bhujbal SP, Cho SJ. Receptor-guided 3D-Quantitative Structure-Activity Relationship and Docking Studies of 6-Substituted 2-Arylaminopurines as CDK2 Kinase Inhibitors. B KOREAN CHEM SOC 2017. [DOI: 10.1002/bkcs.11280] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Seketoulie Keretsu
- Department of Biomedical Sciences, College of Medicine; Chosun University; Gwangju 501-759 Republic of Korea
| | | | - Swapnil Pandurang Bhujbal
- Department of Biomedical Sciences, College of Medicine; Chosun University; Gwangju 501-759 Republic of Korea
| | - Seung Joo Cho
- Department of Biomedical Sciences, College of Medicine; Chosun University; Gwangju 501-759 Republic of Korea
- Department of Cellular and Molecular Medicine, College of Medicine; Chosun University; Gwangju 501-759 Republic of Korea
| |
Collapse
|
12
|
Arba M, Ihsan S, Tri Wahyudi S, Tjahjono DH. Molecular modeling of cationic porphyrin-anthraquinone hybrids as DNA topoisomerase IIβ inhibitors. Comput Biol Chem 2017; 71:129-135. [PMID: 29153891 DOI: 10.1016/j.compbiolchem.2017.10.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 09/14/2017] [Accepted: 10/05/2017] [Indexed: 12/17/2022]
Abstract
Human DNA Topoisomerase II has been regarded as a promising target in anticancer drug discovery. In the present study, we designed six porphyrin-anthraquinone hybrids bearing pyrazole or pyridine group as meso substituents and evaluated their potentials as DNA Topoisomerase IIβ inhibitor. First, we investigated the binding orientation of porphyrin hybrids into DNA topoisomerase IIβ employing AutoDock 4.2 and then performed 20-ns molecular dynamics simulations to see the dynamic stability of each porphyrin-Topo IIβ complex using Amber 14. We found that the binding of porphyrin hybrids occured through intercalation and groove binding mode in addition interaction with the amino acid residues constituting the active cavity of Topo IIβ. Each porphyrin-Topo IIβ complex was stabilized during 20-ns dynamics simulations. The MM-PBSA free energy calculation shows that the binding affinities of porphyrin hybrids were modified with the number of meso substituent. Interestingly, the affinity of all porphyrin hybrids to Topo IIβ was stronger than that of native ligand (EVP), indicating the potential of the designed porphyrin to be considered in experimental research.
Collapse
Affiliation(s)
- Muhammad Arba
- Faculty of Pharmacy, Halu Oleo University, Kendari, 93231, Indonesia.
| | - Sunandar Ihsan
- Faculty of Pharmacy, Halu Oleo University, Kendari, 93231, Indonesia
| | | | - Daryono H Tjahjono
- School of Pharmacy, Bandung Institute of Technology, Bandung, 40312, Indonesia
| |
Collapse
|