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Oduselu GO, Elebiju OF, Ogunnupebi TA, Akash S, Ajani OO, Adebiyi E. Employing Hexahydroquinolines as PfCDPK4 Inhibitors to Combat Malaria Transmission: An Advanced Computational Approach. Adv Appl Bioinform Chem 2024; 17:83-105. [PMID: 39345873 PMCID: PMC11430315 DOI: 10.2147/aabc.s476404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Accepted: 09/18/2024] [Indexed: 10/01/2024] Open
Abstract
Background Existing antimalarial drugs primarily target blood-stage parasites, but there is a need for transmission-blocking drugs to combat malaria effectively. Plasmodium falciparum Calcium-dependent Protein Kinase 4 (CDPK4) is a promising target for such drugs. This study employed advanced in silico analyses of hexahydroquinolines (HHQ) derivatives to identify PfCDPK4 inhibitors capable of disrupting malaria transmission. Structure-based virtual screening (SBVS) was employed to discover HHQ derivatives with the highest binding affinities against the 3D structure of PfCDPK4 (PDB 1D: 4QOX). Methods Interaction analysis of protein-ligand complexes utilized Discovery Studio Client, while druglikeness and ADMET properties were assessed using SwissADME and pkCSM web servers, respectively. Quantum mechanical calculations of the top hits were conducted using density functional theory (DFT), and GROMACS was employed to perform the molecular dynamics (MD) simulations. Binding free energy was predicted using the MMPBSA.py tool from the AMBER package. Results SBVS identified ten best hits possessing docking scores within the range of -11.2 kcal/mol and -10.6 kcal/mol, surpassing the known inhibitor, BKI-1294 (-9.9 kcal/mol). Among these, 4-[4-(Furan-2-carbonyl)piperazin-1-yl]-1-(naphthalen-2-ylmethyl)-2-oxo-4a,5,6,7,8,8a-hexahydroquinoline-3-carbonitrile (PubChem ID: 145784778) exhibited the highest binding affinity (-11.2 kcal/mol) against PfCDPK4. Conclusion Comparative analysis of this compound with BKI-1294 using advanced computational approaches demonstrated competitive potential. These findings suggest the potential of 4-[4-(Furan-2-carbonyl)piperazin-1-yl]-1-(naphthalen-2-ylmethyl)-2-oxo-4a,5,6,7,8,8a-hexahydroquinoline-3-carbonitrile as a promising PfCDPK4 inhibitor for disrupting malaria transmission. However, further experimental studies are warranted to validate its efficacy and safety profile.
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Affiliation(s)
- Gbolahan O Oduselu
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, OG, Nigeria
| | - Oluwadunni F Elebiju
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, OG, Nigeria
- Department of Chemistry, Covenant University, Ota, OG, Nigeria
| | - Temitope A Ogunnupebi
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, OG, Nigeria
- Department of Chemistry, Covenant University, Ota, OG, Nigeria
| | - Shopnil Akash
- Department of Pharmacy, Daffodil International University, Dhaka, Bangladesh
| | - Olayinka O Ajani
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, OG, Nigeria
- Department of Chemistry, Covenant University, Ota, OG, Nigeria
| | - Ezekiel Adebiyi
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, OG, Nigeria
- African Center of Excellence in Bioinformatics & Data Intensive Science, Makerere University, Kampala, Uganda
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
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Quayum ST, Esha NJI, Siraji S, Abbad SSA, Alsunaidi ZH, Almatarneh MH, Rahman S, Alodhayb AN, Alibrahim KA, Kawsar SM, Uddin KM. Exploring the effectiveness of flavone derivatives for treating liver diseases: Utilizing DFT, molecular docking, and molecular dynamics techniques. MethodsX 2024; 12:102537. [PMID: 38299040 PMCID: PMC10828815 DOI: 10.1016/j.mex.2023.102537] [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: 11/01/2023] [Accepted: 12/24/2023] [Indexed: 02/02/2024] Open
Abstract
In exploring nature's potential in addressing liver-related conditions, this study investigates the therapeutic capabilities of flavonoids. Utilizing in silico methodologies, we focus on flavone and its analogs (1-14) to assess their therapeutic potential in treating liver diseases. Molecular change calculations using density functional theory (DFT) were conducted on these compounds, accompanied by an evaluation of each analog's physiochemical and biochemical properties. The study further assesses these flavonoids' binding effectiveness and locations through molecular docking studies against six target proteins associated with human cancer. Tropoflavin and taxifolin served as reference drugs. The structurally modified flavone analogs (1-14) displayed a broad range of binding affinities, ranging from -7.0 to -9.4 kcal mol⁻¹, surpassing the reference drugs. Notably, flavonoid (7) exhibited significantly higher binding affinities with proteins Nrf2 (PDB:1 × 2 J) and DCK (PDB:1 × 2 J) (-9.4 and -8.1 kcal mol⁻¹) compared to tropoflavin (-9.3 and -8.0 kcal mol⁻¹) and taxifolin (-9.4 and -7.1 kcal mol⁻¹), respectively. Molecular dynamics (MD) simulations revealed that the docked complexes had a root mean square deviation (RMSD) value ranging from 0.05 to 0.2 nm and a root mean square fluctuation (RMSF) value between 0.35 and 1.3 nm during perturbation. The study concludes that 5,7-dihydroxyflavone (7) shows substantial promise as a potential therapeutic agent for liver-related conditions. However, further validation through in vitro and in vivo studies is necessary. Key insights from this study include:•Screening of flavanols and their derivatives to determine pharmacological and bioactive properties using ADMET, molinspiration, and pass prediction analysis.•Docking of shortlisted flavone derivatives with proteins having essential functions.•Analysis of the best protein-flavonoid docked complexes using molecular dynamics simulation to determine the flavonoid's efficiency and stability within a system.
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Affiliation(s)
- Syeda Tasnim Quayum
- Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka 1217, Bangladesh
| | - Nusrat Jahan Ikbal Esha
- Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka 1217, Bangladesh
| | - Siam Siraji
- Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka 1217, Bangladesh
| | - Sanaa S. Al Abbad
- Department of Chemistry, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Zainab H.A. Alsunaidi
- Department of Chemistry, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | | | - Shofiur Rahman
- Biological and Environmental Sensing Research Unit, King Abdullah Institute for Nanotechnology, King Saud University, Riyadh 11451, Saudi Arabia
| | - Abdullah N. Alodhayb
- Biological and Environmental Sensing Research Unit, King Abdullah Institute for Nanotechnology, King Saud University, Riyadh 11451, Saudi Arabia
| | - Khuloud A. Alibrahim
- Department of Chemistry, Princess Nora bint Abdulrahman University, College of Science, Riyadh, Al Riyadh, 11671, Saudi Arabia
| | - Sarkar M.A. Kawsar
- Lab of Carbohydrate and Nucleoside Chemistry, Department of Chemistry, University of Chittagong, Chittagong 4331, Bangladesh
| | - Kabir M. Uddin
- Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka 1217, Bangladesh
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Ravindar L, Hasbullah SA, Rakesh KP, Hassan NI. Triazole hybrid compounds: A new frontier in malaria treatment. Eur J Med Chem 2023; 259:115694. [PMID: 37556947 DOI: 10.1016/j.ejmech.2023.115694] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/20/2023] [Accepted: 07/28/2023] [Indexed: 08/11/2023]
Abstract
Reviewing the advancements in malaria treatment, the emergence of triazole hybrid compounds stands out as a groundbreaking development. Combining the advantages of triazole and other moieties, these hybrid compounds offer a new frontier in the battle against malaria. Their potential as effective antimalarial agents has captured the attention of researchers and holds promise for overcoming the challenges posed by drug-resistant malaria strains. We focused on their broad spectrum of antimalarial activity of diverse hybridized 1,2,3-triazoles and 1,2,4-triazoles, structure-activity relationship (SAR), drug-likeness, bioavailability and pharmacokinetic properties reported since 2018 targeting multiple stages of the Plasmodium life cycle. This versatility makes them highly effective against both drug-sensitive and drug-resistant strains of P. falciparum, making them invaluable tools in regions where resistance is prevalent. The synergistic effects of combining the triazole moiety with other pharmacophores have resulted in even greater antimalarial potency. This approach has the potential to circumvent existing resistance mechanisms and provide a more sustainable solution to malaria treatment. While triazole hybrid compounds show great promise, further research and clinical trials are warranted to fully evaluate their safety, efficacy and long-term effects. As research progresses, these compounds can potentially revolutionize the field and contribute to global efforts to eradicate malaria, ultimately saving countless lives worldwide.
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Affiliation(s)
- Lekkala Ravindar
- Department of Chemical Sciences, Universiti Kebangsaan Malaysia (UKM), Bangi, 43600, Selangor, Malaysia
| | - Siti Aishah Hasbullah
- Department of Chemical Sciences, Universiti Kebangsaan Malaysia (UKM), Bangi, 43600, Selangor, Malaysia
| | - K P Rakesh
- Department of Radiology, Biomedical Research Imaging Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Nurul Izzaty Hassan
- Department of Chemical Sciences, Universiti Kebangsaan Malaysia (UKM), Bangi, 43600, Selangor, Malaysia.
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Oduselu GO, Aderohunmu DV, Ajani OO, Elebiju OF, Ogunnupebi TA, Adebiyi E. Synthesis, in silico and in vitro antimicrobial efficacy of substituted arylidene-based quinazolin-4(3 H)-one motifs. Front Chem 2023; 11:1264824. [PMID: 37818483 PMCID: PMC10561392 DOI: 10.3389/fchem.2023.1264824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 09/04/2023] [Indexed: 10/12/2023] Open
Abstract
Introduction: Quinazolin-4(3H)-one derivatives have attracted considerable attention in the pharmacological profiling of therapeutic drug targets. The present article reveals the development of arylidene-based quinazolin-4(3H)-one motifs as potential antimicrobial drug candidates. Methods: The synthetic pathway was initiated through thermal cyclization of acetic anhydride on anthranilic acid to produce 2-methyl-4H-3,1-benzoxazan-4-one 1, which (upon condensation with hydrazine hydrate) gave 3-amino-2-methylquinazolin-4(3H)-one 2. The reaction of intermediate 2 at its amino side arm with various benzaldehyde derivatives furnished the final products, in the form of substituted benzylidene-based quinazolin-4(3H)-one motifs 3a-l, and with thiophene-2-carbaldehyde to afford 3 m. The purified targeted products 3a-m were effectively characterized for structural authentication using physicochemical parameters, microanalytical data, and spectroscopic methods, including IR, UV, and 1H- and 13C-NMR, as well as mass spectral data. The substituted arylidene-based quinazolin-4(3H)-one motifs 3a-m were screened for both in silico and in vitro antimicrobial properties against selected bacteria and fungi. The in silico studies carried out consisted of predicted ADMET screening, molecular docking, and molecular dynamics (MD) simulation studies. Furthermore, in vitro experimental validation was performed using the agar diffusion method, and the standard antibacterial and antifungal drugs used were gentamicin and ketoconazole, respectively. Results and discussion: Most of the compounds possessed good binding affinities according to the molecular docking studies, while MD simulation revealed their levels of structural stability in the protein-ligand complexes. 2-methyl-3-((thiophen-2-ylmethylene)amino) quinazolin-4(3H)-one 3 m emerged as both the most active antibacterial agent (with an minimum inhibitory concentration (MIC) value of 1.95 μg/mL) against Staphylococcus aureus and the most active antifungal agent (with an MIC value of 3.90 μg/mL) against Candida albicans, Aspergillus niger, and Rhizopus nigricans.
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Affiliation(s)
- Gbolahan O. Oduselu
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, Nigeria
| | - Damilola V. Aderohunmu
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, Nigeria
| | - Olayinka O. Ajani
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, Nigeria
- Department of Chemistry, Covenant University, Ota, Ogun State, Nigeria
| | - Oluwadunni F. Elebiju
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, Nigeria
- Department of Chemistry, Covenant University, Ota, Ogun State, Nigeria
| | - Temitope A. Ogunnupebi
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, Nigeria
- Department of Chemistry, Covenant University, Ota, Ogun State, Nigeria
| | - Ezekiel Adebiyi
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, Nigeria
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
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Oduselu GO, Afolabi R, Ademuwagun I, Vaughan A, Adebiyi E. Structure-based pharmacophore modeling, virtual screening, and molecular dynamics simulation studies for identification of Plasmodium falciparum 5-aminolevulinate synthase inhibitors. Front Med (Lausanne) 2023; 9:1022429. [PMID: 36714108 PMCID: PMC9877529 DOI: 10.3389/fmed.2022.1022429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 12/23/2022] [Indexed: 01/13/2023] Open
Abstract
Plasmodium falciparum (Pf) 5-aminolevulinic acid synthase (5-ALAS) is an essential enzyme with high selectivity during liver stage development, signifying its potential as a prophylactic antimalarial drug target. The aim of this study was to identify important potential lead compounds which can serve as inhibitors of Pf 5-ALAS using pharmacophore modeling, virtual screening, qualitative structural assessment, in silico ADMET (Absorption, Distribution, Metabolism, Excretion and Toxicity) evaluation and molecular dynamics simulation. The best model of the tertiary structure of Pf 5-ALAS was obtained using MolProbity, while the following databases were explored for the pharmacophore-based virtual screening: CHEMBL, ChemDiv, ChemSpace, MCULE, MCULE-ULTIMATE, MolPort, NCI Open Chemical Repository, LabNetwork and ZINC databases. 2,621 compounds were screened against the modeled Pf 5-ALAS using AutoDock vina. The post-screening analysis was carried out using Discovery Studio while molecular dynamics simulation was performed on the best hits using NAMD-VMD and Galaxy Europe platform. Compound CSMS00081585868 was observed as the best hit with a binding affinity of -9.9 kcal/mol and predicted Ki of 52.10 nM, engaging in seven hydrogen bonds with the target's active site amino acid residues. The in silico ADMET prediction showed that all ten best hits possessed relatively good pharmacokinetic properties. The qualitative structural assessment of the best hit, CSMS00081585868, revealed that the presence of two pyridine scaffolds bearing hydroxy and fluorine groups linked by a pyrrolidine scaffold contributed significantly to its ability to have a strong binding affinity with the receptor. The best hit also showed stability in the active site of Pf 5-ALAS as confirmed from the RMSD obtained during the MD simulation.
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Affiliation(s)
- Gbolahan O. Oduselu
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, Nigeria
- Department of Chemistry, Covenant University, Ota, Ogun State, Nigeria
| | - Rufus Afolabi
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, Nigeria
- Department of Biochemistry, Covenant University, Ota, Ogun State, Nigeria
| | - Ibitayo Ademuwagun
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, Nigeria
- Department of Biochemistry, Covenant University, Ota, Ogun State, Nigeria
| | - Ashley Vaughan
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, United States
| | - Ezekiel Adebiyi
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, Nigeria
- Department of Computer and Information Science, Covenant University, Ota, Ogun State, Nigeria
- Covenant Applied Informatics and Communications ACE (CApIC-ACE), Covenant University, Ota, Ogun State, Nigeria
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
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Saroha B, Kumar G, Kumar R, Kumari M, Kumar S. A minireview of 1,2,3-triazole hybrids with O-heterocycles as leads in medicinal chemistry. Chem Biol Drug Des 2022; 100:843-869. [PMID: 34592059 DOI: 10.1111/cbdd.13966] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 09/02/2021] [Accepted: 09/26/2021] [Indexed: 01/25/2023]
Abstract
Over the past few decades, the dynamic progress in the synthesis and screening of heterocyclic compounds against various targets has made a significant contribution in the field of medicinal chemistry. Among the wide array of heterocyclic compounds, triazole moiety has attracted the attention of researchers owing to its vast therapeutic potential and easy preparation via copper and ruthenium-catalyzed azide-alkyne cycloaddition reactions. Triazole skeletons are found as major structural components in a different class of drugs possessing diverse pharmacological profiles including anti-cancer, anti-bacterial, anti-fungal, anti-viral, anti-oxidant, anti-inflammatory, anti-diabetic, anti-tubercular, and anti-depressant among various others. Furthermore, in the past few years, a significantly large number of triazole hybrids were synthesized with various heterocyclic moieties in order to gain the added advantage of the improved pharmacological profile, overcoming the multiple drug resistance and reduced toxicity from molecular hybridization. Among these synthesized triazole hybrids, many compounds are available commercially and used for treating different infections/disorders like tazobactam and cefatrizine as potent anti-bacterial agents while isavuconazole and ravuconazole as anti-fungal activities to name a few. In this review, we will summarize the biological activities of various 1,2,3-triazole hybrids with copious oxygen-containing heterocycles as lead compounds in medicinal chemistry. This review will be very helpful for researchers working in the field of molecular modeling, drug design and development, and medicinal chemistry.
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Affiliation(s)
- Bhavna Saroha
- Department of Chemistry, Kurukshetra University, Kurukshetra, India
| | - Gourav Kumar
- Department of Chemistry, Kurukshetra University, Kurukshetra, India
| | - Ramesh Kumar
- Department of Chemistry, Kurukshetra University, Kurukshetra, India
| | - Meena Kumari
- Department of Chemistry, Govt. College for Women Badhra, Charkhi Dadri, India
| | - Suresh Kumar
- Department of Chemistry, Kurukshetra University, Kurukshetra, India
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Targeting aurora kinase a (AURKA) in cancer: molecular docking and dynamic simulations of potential AURKA inhibitors. MEDICAL ONCOLOGY (NORTHWOOD, LONDON, ENGLAND) 2022; 39:246. [PMID: 36180808 DOI: 10.1007/s12032-022-01852-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 09/12/2022] [Indexed: 10/14/2022]
Abstract
The Aurora family of serine/threonine kinases in mammals are key regulators of mitotic progression and are commonly upregulated in human tumors. Since AURKA's increased expression has been linked to cancer, AURKA inhibitors could reduce AURKA expression and function as potent therapeutic drugs. The study's objective was to find and categorize inhibitors with a stronger affinity for AURKA. This study also aimed to identify AURKA's expression profile and prognostic significance across pan-cancers. We looked into therapeutic compounds that were structurally comparable to MK8745 for their potential to selectively inhibit AURKA. We used drug likeliness analysis, MD simulation studies to evaluate the therapeutic possibility of screened MK8745 analogues. AURKA was found to be strongly upregulated in several cancers and is linked to worse overall and relapse-free survival. The Molecular docking and dynamic analysis revealed two new MK8745 analogues to be potent AURKA inhibitors with higher binding affinities and stabilities than MK8745. Furthermore, MK8745 analogues are potential replacements for MK8745 because they have strong binding affinity, which is consistent with MDS results, and have appropriate ADMET properties. Through basic, clinical, and preclinical research, the identification of novel compounds may open the door for their prospective use in the prevention of cancer.
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Alshehri B. Expression patterns and therapeutic implications of histone deacetylase-1 across carcinomas: a comprehensive molecular docking and MD simulation study. MEDICAL ONCOLOGY (NORTHWOOD, LONDON, ENGLAND) 2022; 39:209. [PMID: 36175584 DOI: 10.1007/s12032-022-01811-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 07/26/2022] [Indexed: 11/29/2022]
Abstract
Histone deacetylases (HDACs) are a group of enzymes that control the expression of genes by deacetylating lysine residues on histone and nonhistone proteins. They control the expression of several proteins linked to the development and spread of cancer. Deregulation of HDAC1 has been reported across several tumors, and targeting HDAC1 with specific inhibitors has demonstrated a promising therapeutic strategy. Mocetinostat, an HDAC1 inhibitor, is yielding promising results both in vitro and in vivo studies. However, toxicities associated with Mocetinostat limit its therapeutic efficacy, so there is an urgent need to investigate novel HDAC1 inhibitors. The present study aimed to explore novel HDAC1 inhibitors and investigate the expression profile, and the prognostic and diagnostic significance of HDAC1 across pan-cancers. HDAC1 was found overexpressed across several tumors and its high expression signifies worse OS and RFS. Also, the study identified two novel HDAC1 inhibitors using an in-silico approach with high binding affinity for HDAC1 compared to Mocetinostat and formed significantly stable complexes. In conclusion, the study signifies that targeting HDAC1 is a promising therapeutic strategy, and exploring novel therapeutic agents through basic, translational design may lead to their ultimate use in cancer prevention.
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Affiliation(s)
- Bader Alshehri
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Almajmaah, 11952, Kingdom of Saudi Arabia.
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Sofi S, Mehraj U, Qayoom H, Aisha S, Almilaibary A, Alkhanani M, Mir MA. Targeting cyclin-dependent kinase 1 (CDK1) in cancer: molecular docking and dynamic simulations of potential CDK1 inhibitors. Med Oncol 2022; 39:133. [PMID: 35723742 PMCID: PMC9207877 DOI: 10.1007/s12032-022-01748-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 05/09/2022] [Indexed: 12/12/2022]
Abstract
Cell cycle dysregulation is a characteristic hallmark of malignancies, which results in uncontrolled cell proliferation and eventual tumor formation. Cyclin-dependent kinase 1 (CDK1) is a member of the family of cell cycle regulatory proteins involved in cell cycle maintenance. Given that overexpression of CDK1 has been associated with cancer, CDK1 inhibitors may restore equilibrium to the skewed cell cycle system and operate as an effective therapeutic drug. This study aimed to identify and classify inhibitors having a higher affinity for CDK1 and also evaluate the expression pattern and prognostic relevance of CDK1 in a wide range of cancers. We investigated therapeutic molecules structurally similar to dinaciclib for their ability to inhibit CDK1 selectively. To assess the therapeutic potential of screened Dinaciclib analogs, we used drug likeliness analysis, molecular docking, and simulation analysis. CDK1 was found to be highly upregulated across several malignancies and is associated with poor overall and relapse-free survival. Molecular docking and dynamics evaluation identified two novel dinaciclib analogs as potent CDK1 inhibitors with high binding affinity and stability compared to dinaciclib. The results indicate that increased CDK1 expression is associated with decreased OS and RFS. Additionally, dinaciclib analogs are prospective replacements for dinaciclib since they exhibit increased binding affinity, consistent with MDS findings, and have acceptable ADMET qualities. The discovery of new compounds may pave the road for their future application in cancer prevention through basic, preclinical, and clinical research.
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Affiliation(s)
- Shazia Sofi
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar, J&K, 190006, India
| | - Umar Mehraj
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar, J&K, 190006, India
| | - Hina Qayoom
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar, J&K, 190006, India
| | - Shariqa Aisha
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar, J&K, 190006, India
| | - Abdullah Almilaibary
- Department of Family and Community Medicine, Albaha University, Albaha, 65511, Kingdom of Saudi Arabia
| | - Mustfa Alkhanani
- Emergency Service Department, College of Applied Science, AlMaarefa University, Riyadh, 13713, Kingdom of Saudi Arabia
| | - Manzoor Ahmad Mir
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar, J&K, 190006, India.
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Miryala SK, Basu S, Naha A, Debroy R, Ramaiah S, Anbarasu A, Natarajan S. Datasets comprising the quality validations of simulated protein-ligand complexes and SYBYL docking scores of bioactive natural compounds as inhibitors of Mycobacterium tuberculosis protein-targets. Data Brief 2022; 42:108146. [PMID: 35479419 PMCID: PMC9035630 DOI: 10.1016/j.dib.2022.108146] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/29/2022] [Accepted: 04/04/2022] [Indexed: 01/04/2023] Open
Abstract
Docking scores and simulation parameters to study the potency of natural compounds against protein targets in Mycobacterium tuberculosis (Mtb) were retrieved through molecular docking and in-silico structural investigation. The molecular docking datasets comprised 15 natural compounds, seven conventional anti-tuberculosis (anti-TB) drugs and their seven corresponding Mtb target proteins. Mtb protein targets were actively involved in translation mechanism, nucleic acid metabolism and membrane integrity. Standard structural screening and stereochemical optimizations were adopted to generate the 3D protein structures and their corresponding ligands prior to molecular docking. Force-field integration and energy minimization were further employed to obtain the proteins in their ideal geometry. Surflex-dock algorithm using Hammerhead scoring functions were used to finally produce the docking scores between each protein and the corresponding ligand(s). The best-docked complexes selected for simulation studies were subjected to topology adjustments, charge neutralizations, solvation and equilibrations (temperature, volume and pressure). The protein-ligand complexes and molecular dynamics parameter files have been provided. The trajectories of the simulated parameters such as density, pressure and temperature were generated with integrated tools of the simulation suite. The datasets can be useful to computational and molecular medicine researchers to find therapeutic leads relevant to the chemical behaviours of a specific class of compounds against biological systems. Structural parameters and energy functions provided a set of standard values that can be utilised to design simulation experiments regarding similar macromolecular interactions.
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Miryala SK, Basu S, Naha A, Debroy R, Ramaiah S, Anbarasu A, Natarajan S. Identification of bioactive natural compounds as efficient inhibitors against Mycobacterium tuberculosis protein-targets: A molecular docking and molecular dynamics simulation study. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117340] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Basu S, Naha A, Veeraraghavan B, Ramaiah S, Anbarasu A. In silico structure evaluation of BAG3 and elucidating its association with bacterial infections through protein-protein and host-pathogen interaction analysis. J Cell Biochem 2021; 123:115-127. [PMID: 33998043 DOI: 10.1002/jcb.29953] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/11/2021] [Accepted: 05/03/2021] [Indexed: 01/30/2023]
Abstract
BAG3, a co-chaperone protein with a Bcl-2-associated athanogene (BAG) domain, has diverse functionalities in protein-folding, apoptosis, inflammation, and cell cycle regulatory cross-talks. It has been well characterised in cardiac diseases, cancers, and viral pathogenesis. The multiple roles of BAG3 are attributed to its functional regions like BAG, Tryptophan-rich (WW), isoleucine-proline-valine-rich (IPV), and proline-rich (PXXP) domains. However, to study its structural impact on various functions, the experimental 3D structure of BAG3 protein was not available. Hence, the structure was predicted through in silico modelling and validated through computational tools and molecular dynamics simulation studies. To the best of our knowledge, the role of BAG3 in bacterial infections is not explicitly reported. We attempted to study them through an in-silico protein-protein interaction network and host-pathogen interaction analysis. From structure-function relationships, it was identified that the WW and PXXP domains were associated with cellular cytoskeleton rearrangement and adhesion-mediated response, which might be involved in BAG3-related intracellular bacterial proliferation. From functional enrichment analysis, Gene Ontology terms and topological matrices, 18 host proteins and 29 pathogen proteins were identified in the BAG3 interactome pertaining to Legionellosis, Tuberculosis, Salmonellosis, Shigellosis, and Pertussis through differential phosphorylation events associated with serine metabolism. Furthermore, it was evident that direct (MAPK8, MAPK14) and associated (MAPK1, HSPD1, NFKBIA, TLR2, RHOA) interactors of BAG3 could be considered as therapeutic markers to curb down intracellular bacterial propagation in humans.
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Affiliation(s)
- Soumya Basu
- Medical and Biological Computing Laboratory, School of Bio-Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Aniket Naha
- Medical and Biological Computing Laboratory, School of Bio-Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Balaji Veeraraghavan
- Department of Clinical Microbiology, Christian Medical College & Hospital, Vellore, Tamil Nadu, India
| | - Sudha Ramaiah
- Medical and Biological Computing Laboratory, School of Bio-Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Anand Anbarasu
- Medical and Biological Computing Laboratory, School of Bio-Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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13
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Santos KLB, Queiroz AN, Lobato CC, Vale JKL, Santos CBR, Borges RS. A comparative theoretical mechanism on simplified flavonoid derivatives and isoxazolone analogous as Michael system inhibitor. J Mol Model 2021; 27:26. [PMID: 33410998 DOI: 10.1007/s00894-020-04647-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 12/13/2020] [Indexed: 11/29/2022]
Abstract
Flavonoids are a big class of natural product and have a wide range of biological activities. Some of these applications depend on its antioxidant capacity. Nevertheless, another mechanism can be involved by means of alkylation reaction on α,β-unsaturated carbonyl system. This study aimed to evaluate the antioxidant capacity and the chemical reactivity among simplified flavonoid derivatives and isoxazolone analogous as Michael system by using B3LYP functional and 6-311 g(d,p) basis set. Frontier molecular orbital, ionization potential (IP), spin density contributions, and Fukui index explain the antioxidant capacity and reactivity index on isoxazolone and its related derivatives. The best contribution at β-alkene moiety is related to better reactivity of α,β-unsaturated carbonyl group. A decrease in antioxidant capacity is related to an increase in the chemical reactivity index. The frontier molecular orbitals show that aurone is more reactive than isoxazolone. In accordance with Fukui index, isoxazolone can be better inhibitor as Michael system when compared to flavonoid derivatives. Graphical abstract.
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Affiliation(s)
- Kelton L B Santos
- Departamento de Ciências Exatas e Tecnológicas, Universidade Federal do Amapá, Macapá, AP, 68903-419, Brazil. .,Núcleo de Estudos e Seleção de Moléculas Bioativas, Instituto de Ciências da Saúde, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil.
| | - Auriekson N Queiroz
- Núcleo de Estudos e Seleção de Moléculas Bioativas, Instituto de Ciências da Saúde, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil
| | - Cleison C Lobato
- Núcleo de Estudos e Seleção de Moléculas Bioativas, Instituto de Ciências da Saúde, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil.,Campus Binacional, Universidade Federal do Amapá, Oiapoque, AP, 68980-000, Brazil
| | - Joyce K L Vale
- Núcleo de Estudos e Seleção de Moléculas Bioativas, Instituto de Ciências da Saúde, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil
| | - Cleydson B R Santos
- Laboratório de Modelagem e Química Computacional, Departamento de Ciências Biológicas e da Saúde, Universidade Federal do Amapá, Macapá, AP, 68903-419, Brazil
| | - Rosivaldo S Borges
- Núcleo de Estudos e Seleção de Moléculas Bioativas, Instituto de Ciências da Saúde, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil.
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14
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Pramisandi A, Dobashi K, Mori M, Nonaka K, Matsumoto A, Tokiwa T, Higo M, Kristiningrum, Amalia E, Nurkanto A, Inaoka DK, Waluyo D, Kita K, Nozaki T, Ōmura S, Shiomi K. Microbial inhibitors active against Plasmodium falciparum dihydroorotate dehydrogenase derived from an Indonesian soil fungus, Talaromyces pinophilus BioMCC-f.T.3979. J GEN APPL MICROBIOL 2020; 66:273-278. [PMID: 32669511 DOI: 10.2323/jgam.2019.11.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
An Indonesian soil fungus, Talaromyces pinophilus BioMCC-f.T.3979 was cultured to find novel scaffolds of Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) inhibitors. We obtained altenusin (1), which inhibits PfDHODH, with an IC50 value of 5.9 μM, along with other metabolites: mitorubrinol (2) and mitorubrinic acid (3). Compounds 1 and 2 inhibited PfDHODH but displayed no activity against the human orthologue. They also inhibited P. falciparum 3D7 cell growth in vitro. Compound 3 showed little PfDHODH inhibitory activity or cell growth inhibitory activity.
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Affiliation(s)
- Amila Pramisandi
- Graduate School of Infection Control Sciences, Kitasato University.,Laboratory for Biotechnology, Agency for the Assessment and Application of Technology (BPPT)
| | - Kazuyuki Dobashi
- Department of Drug Discovery Sciences, Kitasato Institute for Life Sciences
| | - Mihoko Mori
- Graduate School of Infection Control Sciences, Kitasato University.,Department of Drug Discovery Sciences, Kitasato Institute for Life Sciences
| | - Kenichi Nonaka
- Graduate School of Infection Control Sciences, Kitasato University.,Department of Drug Discovery Sciences, Kitasato Institute for Life Sciences
| | - Atsuko Matsumoto
- Graduate School of Infection Control Sciences, Kitasato University.,Department of Drug Discovery Sciences, Kitasato Institute for Life Sciences
| | - Toshiyuki Tokiwa
- Department of Drug Discovery Sciences, Kitasato Institute for Life Sciences
| | - Mayuka Higo
- Department of Drug Discovery Sciences, Kitasato Institute for Life Sciences
| | - Kristiningrum
- Laboratory for Biotechnology, Agency for the Assessment and Application of Technology (BPPT)
| | - Eri Amalia
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo
| | - Arif Nurkanto
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo.,Research Center for Biology, Indonesia Institute of Sciences (LIPI)
| | - Daniel Ken Inaoka
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo.,School of Tropical Medicine and Global Health, Nagasaki University.,Department of Molecular Infection Dynamics, Institute of Tropical Medicine (NEKKEN), Nagasaki University
| | - Danang Waluyo
- Laboratory for Biotechnology, Agency for the Assessment and Application of Technology (BPPT)
| | - Kiyoshi Kita
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo.,School of Tropical Medicine and Global Health, Nagasaki University.,Department of Molecular Infection Dynamics, Institute of Tropical Medicine (NEKKEN), Nagasaki University
| | - Tomoyoshi Nozaki
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo
| | - Satoshi Ōmura
- Department of Drug Discovery Sciences, Kitasato Institute for Life Sciences
| | - Kazuro Shiomi
- Graduate School of Infection Control Sciences, Kitasato University.,Department of Drug Discovery Sciences, Kitasato Institute for Life Sciences
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15
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Sharma M, Prasher P. An epigrammatic status of the ' azole'-based antimalarial drugs. RSC Med Chem 2020; 11:184-211. [PMID: 33479627 PMCID: PMC7536834 DOI: 10.1039/c9md00479c] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 11/26/2019] [Indexed: 11/21/2022] Open
Abstract
The development of multidrug resistance in the malarial parasite has sabotaged majority of the eradication efforts by restraining the inhibition profile of first line as well as second line antimalarial drugs, thus necessitating the development of novel pharmaceutics constructed on appropriate scaffolds with superior potency against the drug-resistant and drug-susceptible Plasmodium parasite. Over the past decades, the infectious malarial parasite has developed resistance against most of the contemporary therapeutics, thus necessitating the rational development of novel approaches principally focused on MDR malaria. This review presents an epigrammatic collation of the epidemiology and the contemporary antimalarial therapeutics based on the 'azole' motif.
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Affiliation(s)
- Mousmee Sharma
- Department of Chemistry , Uttaranchal University , Dehradun 248007 , India
- UGC Sponsored Centre for Advanced Studies , Department of Chemistry , Guru Nanak Dev University , Amritsar 143005 , India
| | - Parteek Prasher
- Department of Chemistry , University of Petroleum & Energy Studies , Dehradun 248007 , India . ;
- UGC Sponsored Centre for Advanced Studies , Department of Chemistry , Guru Nanak Dev University , Amritsar 143005 , India
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16
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Cheng P, Yang L, Huang X, Wang X, Gong M. Chalcone hybrids and their antimalarial activity. Arch Pharm (Weinheim) 2020; 353:e1900350. [PMID: 32003489 DOI: 10.1002/ardp.201900350] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 01/08/2020] [Accepted: 01/09/2020] [Indexed: 02/06/2023]
Abstract
Malaria, one of the most striking, re-emerging infectious diseases caused by the genus Plasmodium, places a huge burden on global healthcare systems. A major challenge in the control and eradication of malaria is the continuous emergence of increasingly widespread drug-resistant malaria, creating an urgent need to develop novel antimalarial agents. Chalcone derivatives are ubiquitous in nature and have become indispensable units in medicinal chemistry applications due to their diverse biological profiles. Many chalcone derivatives demonstrate potential in vitro and in vivo antimalarial activity, so chalcone could be a useful template for the development of novel antimalarial agents. This review covers the recent development of chalcone hybrids as antimalarial agents. The critical aspects of the design and structure-activity relationship of these compounds are also discussed.
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Affiliation(s)
- Peng Cheng
- Shandong Institute of Parasitic Diseases, Shandong First Medical University & Shandong Academy of Medical Sciences, Jining, Shandong, China
| | - Linlin Yang
- Department of Vector Biological Control, Jining Municipal Center for Disease Control and Prevention, Jining, Shandong, China
| | - Xiaodan Huang
- Shandong Institute of Parasitic Diseases, Shandong First Medical University & Shandong Academy of Medical Sciences, Jining, Shandong, China
| | - Xuejun Wang
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, China
| | - Maoqing Gong
- Shandong Institute of Parasitic Diseases, Shandong First Medical University & Shandong Academy of Medical Sciences, Jining, Shandong, China
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17
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Kanipakam H, Sharma K, Thinlas T, Mohammad G, Pasha MAQ. Structural and functional alterations of nitric oxide synthase 3 due to missense variants associate with high-altitude pulmonary edema through dynamic study. J Biomol Struct Dyn 2020; 39:294-309. [PMID: 31902292 DOI: 10.1080/07391102.2019.1711190] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The human endothelial nitric oxide synthase (NOS3) is 28 Kbp at 7q36.1 and encodes protein comprising of 1280 amino acids. Being a major source of nitric oxide, the enzyme is crucial to the vascular homeostasis and thereby to be an important pharmaceutical target. We hence have been investigating this molecule in a high-altitude disorder namely, high-altitude pulmonary edema (HAPE). We performed a genome-wide association study (GWAS) in a case-control design of sojourners that included healthy controls and HAPE patients (n = 200) each. Four NOS3 missense SNPs i.e. rs1799983 (E298D), rs3918232 (V827M), rs3918201 (R885M) and rs3918234 (Q982L), were associated significantly with HAPE (P-value < 0.05). Furthermore, extensive in silico analyses were performed to predict the detrimental effect of the four variant types and their three most relevant co-factors namely, heme, flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN) that are accountable for amendment of protein stability leading to structural de-construction. Subsequently, we validated the findings in a larger sample size of the two study groups. HAPE patients had a higher frequency of the four variants and significantly decreased levels of circulating nitric oxide (NO) (P-value < 0.001). The in silico and human subjects findings complement each other. This study explored the impact of HAPE-associated NOS3 variants with its protein structure stability and holds promise to be current and future drug targets.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hema Kanipakam
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Kavita Sharma
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Tashi Thinlas
- Department of Medicine, SNM Hospital, Leh, Ladakh, India
| | | | - M A Qadar Pasha
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
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18
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Rawat R, Verma SM. An exclusive computational insight toward molecular mechanism of MMV007571, a multitarget inhibitor of Plasmodium falciparum. J Biomol Struct Dyn 2019; 38:5362-5373. [PMID: 31790334 DOI: 10.1080/07391102.2019.1700165] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Recently, two Malaria Box molecules namely MMV007571 and MMV020439 well known inhibitors of New Permeability Pathway (NPP) function also showed a secondary phenotype of inhibition of enzyme Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) and cytochrome bc1 complex in metabolic profile assays. Intricacies of their binding at the newly identified targets was need of the hour which motivated us to study their binding using molecular docking and dynamics simulations approach. Interestingly, molecular docking results of both MMV007571 and MMV020439 showed good binding affinity toward the Qo site of cytochrome bc1 complex while only MMV007571 illustrated notable binding characterstics for PfDHODH. Molecular Dynamics (MD) simulations when carried out for native-PfDHODH, PfDHODH-MMV007571 and PfDHODH-Genz667348 models (100 ns each) demonstrated the role of inhibitors over the N-terminus domain which experienced conformational transition from an open state (22 Å) to closed state (16 Å) in the protein-inhibitor models. Dynamics also indicated that the loop domain near cofactor flavin mononucleotide (FMN) attained more felxibility which further lead to its poor binding and may contribute to inhibition of the oxidation (catalytic) process. Moreover, the pharmacophoric features of MMV007571 was justified and may serve as a template for the design of novel series of more potent multitarget inhibitors against Plasmodium falciparum.AbbreviationsÅAngstromACTsArtemisinin combination therapiescyt bc1cytochrome bc1 complexhhour(s)KKelvinµMmicromolarMMVMedicine for malaria ventureNLucNanoluciferasenMnanomolarNPPNew permeation pathwayPDBProtein data bankPfDHODHPlasmodium falciparum dihydroorotate dehydrogenasePOPC1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholineRBCRed blood corpusclesRMSDRoot-mean-square deviationSPStandard precisionvdWvan der WaalsXPExtra precisionyDHODHYeast dihydroorotate dehydrogenaseCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ravi Rawat
- Department of Pharmaceutical Sciences and Technology, Birla Institute of Technology, Mesra, Ranchi, India
| | - Saurabh M Verma
- Department of Pharmaceutical Sciences and Technology, Birla Institute of Technology, Mesra, Ranchi, India
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19
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Thillainayagam M, Ramaiah S, Anbarasu A. Molecular docking and dynamics studies on novel benzene sulfonamide substituted pyrazole-pyrazoline analogues as potent inhibitors of Plasmodium falciparum Histo aspartic protease. J Biomol Struct Dyn 2019; 38:3235-3245. [PMID: 31411122 DOI: 10.1080/07391102.2019.1654923] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Malaria is the major health issue in African, Asian and Mediterranean regions of the world. Due to the emerging resistance by the parasites and mosquitoes for the current medications and insecticides, respectively, the malaria free human world can be attained only by the novel design and development of new anti-malarial drugs. Hence, we attempted to carry out in silico screening of benzene sulfonamide substituted pyrazole-pyrazoline series against Histo aspartic protease. Our results reveal that the 65% of the data set with the free binding energy in the range of -11.58 to -11.21 kcal/mol, which is categorized as 'high scoring'. Ligands are docked with the catalytic residues Asp 215, Ser 75, Thr 33 and Ala 217, respectively. Molecular dynamic simulation study of free enzyme and the enzyme complex with 4-(5-(4-methoxyphenyl)-1'phenyl-3'-(p-tolyl)-3,4-1'H,2H-[3,4'-bipyrazol]-2-yl)benezenesulfonamide indicated structural stability. The trajectory analysis of complex reveals that the HAP-ligand complex is more stable than the free HAP. We are of the opinion that our results will be useful for designing potential anti-malarial compounds. AbbreviationsADTauto dock toolsBSPPbenzene sulfonamide substituted pyrazole-pyrazolineCQchloroquineHAPhisto aspartic proteaseKKelvinMDmolecular dockingMM/PBSAmolecular mechanics/Poisson Boltzmann surface areaNVTnormal volume and temperatureNPTnormal pressure and temperatureNsnanosecondsPDBprotein data bank.pdbprogram data base formatP. falciparumPlasmodium falciparumPspicosecondsPMsplasmepsinsP. vivaxPlasmodium vivaxRgradius of gyrationRMSDroot mean square deviationRMSFroot mean square fluctuationWHOWorld Health OrganizationCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mahalakshmi Thillainayagam
- Medical & Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Sudha Ramaiah
- Medical & Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Anand Anbarasu
- Medical & Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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20
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Ragunathan A, Malathi K, Ramaiah S, Anbarasu A. FtsA as a cidal target for Staphylococcus aureus: Molecular docking and dynamics studies. J Cell Biochem 2019; 120:7751-7758. [PMID: 30417432 DOI: 10.1002/jcb.28049] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 10/22/2018] [Indexed: 01/24/2023]
Abstract
Staphylococcus aureus infection is a healthcare problem to mankind for a considerable period of time. Once when it enters the bloodstream of an individual, it may potentially result in life-threatening conditions. The resistance of S. aureus to various drugs such as penicillin, methicillin, gentamicin, erythromycin, and tetracycline have been well documented. Presently vancomycin is the drug of choice for methicillin resistant S. aureus. Scientists believe that S. aureus would completely develop resistance to vancomycin as well. Therefore there is a commensurate need to develop a drug to replace vancomycin. In the current study, we have focussed on FtsA, an important and vital cell division protein, which is found only in S. aureus and in other prokaryotic cells. We have carried out virtual screening process for FtsA against ZINC database, the best hit molecules obtained from the preliminary docking studies were subjected to SYBYL X 2.0 docking. The molecules ZINC74432848, ZINC37769607, and ZINC96896268 displayed the highest C-score value of 4.89, 4.49, and 4.22, respectively. The top ranked molecule ZINC74432848 was observed to form 4 hydrogen bonds with FtsA. The simulation study reveals the greater stability of the FtsA-ZINC74432848 complex. If the in vitro and in vivo study turns out affirmative, then ZINC74432848 could be developed as a potent drug for FtsA.
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Affiliation(s)
- Adhithya Ragunathan
- Department of Biotechnology, Medical & Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Kullappan Malathi
- Department of Biotechnology, Medical & Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Sudha Ramaiah
- Department of Biotechnology, Medical & Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Anand Anbarasu
- Department of Biotechnology, Medical & Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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21
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Malathi K, Anbarasu A, Ramaiah S. Identification of potential inhibitors for Klebsiella pneumoniae carbapenemase-3: a molecular docking and dynamics study. J Biomol Struct Dyn 2019; 37:4601-4613. [PMID: 30632921 DOI: 10.1080/07391102.2018.1556737] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Klebsiella pneumoniae (K. pneumoniae) is a Gram-negative bacterium, which is a leading causal agent for nosocomial infections. Penicillin, cephalosporin and carbapenems along with the inhibitors such as tazobactam, sulbactam and clavulanic acid are prescribed for the treatment of K. pneumoniae infections. Prolonged exposure to β-lactam antibiotics leads to the development of resistance. The major reason for the β-lactam resistance in K. pneumoniae is the secretion of the enzyme K. pneumoniae carbapenemase (KPC). Secretion of KPC-2 and its variant KPC-3 by the K. pneumoniae strains causes resistance to both the substrate imipenem and the β-lactamase inhibitors. Hence, molecular docking and dynamics studies were carried out to analyze the resistance mechanism of KPC-2-imipenem and KPC-3-imipenem at the structural level. It reveals that KPC-3-imipenem has the highest c-score value of 4.03 with greater stability than the KPC-2-imipenem c-score value of 2.36. Greater the interaction between the substrate and the β-lactamase enzyme, higher the chances of hydrolysis of the substrate. Presently available β-lactamase inhibitors are also ineffective against KPC-3-expressing strains. This situation necessitates the need for development of novel and effective inhibitors for KPC-3. We have carried out the virtual screening process to identify more effective inhibitors for KPC-3, and this has resulted in ZINC48682523, ZINC50209041 and ZINC50420049 as the best binding energy compounds, having greater binding affinity and stability than KPC-3-tazobactam interactions. Our study provides a clear understanding of the mechanism of drug resistance and provides valuable inputs for the development of inhibitors against KPC-3 expressing K. pneumoniae. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kullappan Malathi
- Medical & Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology , Vellore , Tamil Nadu , India
| | - Anand Anbarasu
- Medical & Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology , Vellore , Tamil Nadu , India
| | - Sudha Ramaiah
- Medical & Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology , Vellore , Tamil Nadu , India
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22
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Thillainayagam M, Malathi K, Anbarasu A, Singh H, Bahadur R, Ramaiah S. Insights on inhibition of Plasmodium falciparum plasmepsin I by novel epoxyazadiradione derivatives – molecular docking and comparative molecular field analysis. J Biomol Struct Dyn 2018. [DOI: 10.1080/07391102.2018.1510342 pmid: 30092746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Mahalakshmi Thillainayagam
- Medical & Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Kullappan Malathi
- Medical & Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Anand Anbarasu
- Medical & Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | | | - Renu Bahadur
- Indian Council for Medical Research, New Delhi, India
| | - Sudha Ramaiah
- Medical & Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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23
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Thillainayagam M, Malathi K, Anbarasu A, Singh H, Bahadur R, Ramaiah S. Insights on inhibition of Plasmodium falciparum plasmepsin I by novel epoxyazadiradione derivatives – molecular docking and comparative molecular field analysis. J Biomol Struct Dyn 2018; 37:3168-3182. [DOI: 10.1080/07391102.2018.1510342] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Mahalakshmi Thillainayagam
- Medical & Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Kullappan Malathi
- Medical & Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Anand Anbarasu
- Medical & Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | | | - Renu Bahadur
- Indian Council for Medical Research, New Delhi, India
| | - Sudha Ramaiah
- Medical & Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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24
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Malathi K, Ramaiah S. Mechanism of imipenem resistance in metallo‐β‐lactamases expressing pathogenic bacterial spp. and identification of potential inhibitors: An in silico approach. J Cell Biochem 2018; 120:584-591. [DOI: 10.1002/jcb.27414] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 07/12/2018] [Indexed: 12/27/2022]
Affiliation(s)
- Kullappan Malathi
- Medical and Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology Vellore Tamil Nadu India
| | - Sudha Ramaiah
- Medical and Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology Vellore Tamil Nadu India
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Malathi K, Ramaiah S. Bioinformatics approaches for new drug discovery: a review. Biotechnol Genet Eng Rev 2018; 34:243-260. [DOI: 10.1080/02648725.2018.1502984] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Kullappan Malathi
- Medical & Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Sudha Ramaiah
- Department of Biosciences, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu
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Mahapatra DK, Ghorai S, Bharti SK, Patil AG, Gayen S. Current Discovery Progress of Some Emerging Anti-infective Chalcones: Highlights from 2016 to 2017. Curr Drug Discov Technol 2018; 17:30-44. [PMID: 30033873 DOI: 10.2174/1570163815666180720170030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 07/06/2018] [Accepted: 07/10/2018] [Indexed: 11/22/2022]
Abstract
The anti-infective potentials of the natural products are very well known for centuries and are a part of traditional healing. The foremost therapeutic classes include flavones, isoflavones, flavonols, flavanones, flavanols, proanthocyanidins, anthocyanidins, chalcones, and aurones. The chalcone or 1,3-diphenyl-2E-propene-1-one represents the class of natural products which are comprised of benzylideneacetophenone function; i.e. two aromatic moieties linked together by an α, β-unsaturated carbonyl bridge comprising three-carbons. At present, chalcone is one of the privileged scaffolds that can be synthesized in the laboratory to derive different pharmacologically active compounds. This article is the continued form of the previously published work on anti-infective perspectives of chalcones (highlighted till 2015). The current work emphasizes on the discovery process of the chalcone in the period of 2016 to 2017 on malaria, trypanosomiasis, leishmaniasis, filaria, tuberculosis, netamodes, Human Immunodeficiency Virus (HIV), Tobacco Mosaic Virus (TMV), Severe Acute Respiratory Syndrome (SARS), and miscellaneous conditions. This review comprehensively focuses on the latest progress related with the anti-infective chalcones. The content includes the crucial structural features of chalcone scaffold including structure-activity relationship(s) along with their plausible mechanism of action(s) from the duration Jan 2016 to Dec 2017. This literature will be of prime interest to medicinal chemists in getting ideas and concepts for better rational development of potential anti-infective inhibitors.
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Affiliation(s)
- Debarshi K Mahapatra
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Sciences, Dr. Hari Singh Gour Vishwavidyalaya (A Central University), Sagar 470003, Madhya Pradesh, India
| | - Soumajit Ghorai
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Sciences, Dr. Hari Singh Gour Vishwavidyalaya (A Central University), Sagar 470003, Madhya Pradesh, India
| | - Sanjay K Bharti
- Institute of Pharmaceutical Sciences, Guru Ghasidas Vishwavidyalaya (A Central University), Bilaspur 495009, Chhattisgarh, India
| | - Asmita G Patil
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Sciences, Dr. Hari Singh Gour Vishwavidyalaya (A Central University), Sagar 470003, Madhya Pradesh, India
| | - Shovanlal Gayen
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Sciences, Dr. Hari Singh Gour Vishwavidyalaya (A Central University), Sagar 470003, Madhya Pradesh, India
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