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Yilmaz A, Koca M, Ercan S, Acar OO, Boga M, Sen A, Kurt A. Amelioration potential of synthetic oxime chemical cores against multiple sclerosis and Alzheimer's diseases: Evaluation in aspects of in silico and in vitro experiments. J Mol Struct 2024; 1318:139193. [DOI: 10.1016/j.molstruc.2024.139193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2024]
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2
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Aparecida Dos Santos France F, Maeda DK, Rodrigues AB, Ono M, Lopes Nogueira Marchetti F, Marchetti MM, Faustino Martins AC, Gomes RDS, Rainho CA. Exploring fatty acids from royal jelly as a source of histone deacetylase inhibitors: from the hive to applications in human well-being and health. Epigenetics 2024; 19:2400423. [PMID: 39255363 PMCID: PMC11404605 DOI: 10.1080/15592294.2024.2400423] [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: 05/05/2024] [Revised: 08/17/2024] [Accepted: 08/30/2024] [Indexed: 09/12/2024] Open
Abstract
A differential diet with royal jelly (RJ) during early larval development in honeybees shapes the phenotype, which is probably mediated by epigenetic regulation of gene expression. Evidence indicates that small molecules in RJ can modulate gene expression in mammalian cells, such as the fatty acid 10-hydroxy-2-decenoic acid (10-HDA), previously associated with the inhibition of histone deacetylase enzymes (HDACs). Therefore, we combined computational (molecular docking simulations) and experimental approaches for the screening of potential HDAC inhibitors (HDACi) among 32 RJ-derived fatty acids. Biochemical assays and gene expression analyses (Reverse Transcriptase - quantitative Polymerase Chain Reaction) were performed to evaluate the functional effects of the major RJ fatty acids, 10-HDA and 10-HDAA (10-hydroxy-decanoic acid), in two human cancer cell lines (HCT116 and MDA-MB-231). The molecular docking simulations indicate that these fatty acids might interact with class I HDACs, specifically with the catalytic domain of human HDAC2, likewise well-known HDAC inhibitors (HDACi) such as SAHA (suberoylanilide hydroxamic acid) and TSA (Trichostatin A). In addition, the combined treatment with 10-HDA and 10-HDAA inhibits the activity of human nuclear HDACs and leads to a slight increase in the expression of HDAC-coding genes in cancer cells. Our findings indicate that royal jelly fatty acids collectively contribute to HDAC inhibition and that 10-HDA and 10-HDAA are weak HDACi that facilitate the acetylation of lysine residues of chromatin, triggering an increase in gene expression levels in cancer cells.
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Affiliation(s)
| | - Debora Kazumi Maeda
- Department of Chemical and Biological Sciences, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Ana Beatriz Rodrigues
- Department of Chemical and Biological Sciences, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Mai Ono
- Department of Chemical and Biological Sciences, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Franciele Lopes Nogueira Marchetti
- Department of Chemical and Biological Sciences, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Marcos Martins Marchetti
- Department of Chemical and Biological Sciences, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | | | | | - Cláudia Aparecida Rainho
- Department of Chemical and Biological Sciences, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, SP, Brazil
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Ansari WA, Khan MA, Hasan SMM, Siddiqui Z, Ahmad S, Khan MS, Khan MF. Computational screening of chemical constituents derived from berry fruits as allosteric caspace-3/-7 inhibitors. 3 Biotech 2024; 14:234. [PMID: 39297056 PMCID: PMC11405617 DOI: 10.1007/s13205-024-04067-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Accepted: 08/23/2024] [Indexed: 09/21/2024] Open
Abstract
With the aim of finding the plant-derived allosteric inhibitors of caspase-3/-7, we conducted computational investigations of bioactive compounds present in various berry fruits. In a molecular docking study, perulactone demonstrated excellent binding affinity scores of -12.1 kcal/mol and -9.1 kcal/mol for caspase 7 and 3, respectively, whereas FDA-approved allosteric inhibitors (DICA and FICA) were found to show lower docking scores (-5.6 and -6.1 kcal/mol) against caspase 7 while (-5.0 and -5.1 kcal/mol) for caspase 3, respectively. MD simulations were used to validate the binding stability of perulactone in the active sites of caspase-7/-3, and the results showed outstanding stability with lower ligand RMSDs of 1.270-3.088 Å and 2.426-9.850 Å against the targeted receptor. Furthermore, we performed MMGBSA free binding energy, where the perulactone values of ΔG Bind were determined to be -63.98 kcal/mol and -66.32 kcal/mol for both receptors (3IBF and 1NME), which are significantly better than the -45.16 kcal/mol and -39.51 kcal/mol for DICA as well as -26.37 kcal/mol and -15.50 kcal/mol for FICA, respectively. The drug resemblance of perulactone was effectively evaluated by ADMET. Thus, our findings indicated that perulactone could be an orally administered therapeutic candidate for regulating apoptosis in a variety of disorders. However, there may be an urgent need to study using in vitro and in vivo experiments. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-024-04067-7.
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Affiliation(s)
- Waseem Ahmad Ansari
- Department of Biotechnology, Era's Lucknow Medical College & Hospital, Era University, Sarfarazganj, Hardoi Road, Lucknow, 226003 India
| | - Mohsin Ali Khan
- Center for Disease Mapping and Therapeutic Research, Era's Lucknow Medical College & Hospital, Era University, Sarfarazganj, Hardoi Road, Lucknow, 226003 India
| | - S M Mahfooz Hasan
- Center for Disease Mapping and Therapeutic Research, Era's Lucknow Medical College & Hospital, Era University, Sarfarazganj, Hardoi Road, Lucknow, 226003 India
| | - Zainab Siddiqui
- Center for Disease Mapping and Therapeutic Research, Era's Lucknow Medical College & Hospital, Era University, Sarfarazganj, Hardoi Road, Lucknow, 226003 India
| | - Saheem Ahmad
- Department of Medical Laboratory Science, College of Applied Medical Sciences, University of Hail, 2440 Hail, Saudi Arabia
| | - Mohd Shahnawaz Khan
- Department of Biochemistry, College of Sciences, King Saud University, 12371 Riyadh, Saudi Arabia
| | - Mohammad Faheem Khan
- Department of Biotechnology, Era's Lucknow Medical College & Hospital, Era University, Sarfarazganj, Hardoi Road, Lucknow, 226003 India
- Department of Chemistry, Era University, Sarfarazganj, Hardoi Road, Lucknow, 226003 India
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Chen L, Zhang L, Li Y, Qiao L, Kumar S. Screening of promising molecules against potential drug targets in Yersinia pestis by integrative pan and subtractive genomics, docking and simulation approach. Arch Microbiol 2024; 206:415. [PMID: 39320535 DOI: 10.1007/s00203-024-04140-y] [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: 07/19/2024] [Revised: 09/02/2024] [Accepted: 09/10/2024] [Indexed: 09/26/2024]
Abstract
This study focuses on Yersinia pestis, the bacterium responsible for plague, which posed a severe threat to public health in history. Despite the availability of antibiotics treatment, the emergence of antibiotic resistance in this pathogen has increased challenges of controlling the infections and plague outbreaks. The development of new drug targets and therapies is urgently needed. This research aims to identify novel protein targets from 28 Y. pestis strains by the integrative pan-genomic and subtractive genomics approach. Additionally, it seeks to screen out potential safe and effective alternative therapies against these targets via high-throughput virtual screening. Targets should lack homology to human, gut microbiota, and known human 'anti-targets', while should exhibit essentiality for pathogen's survival and virulence, druggability, antibiotic resistance, and broad spectrum across multiple pathogenic bacteria. We identified two promising targets: the aminotransferase class I/class II domain-containing protein and 3-oxoacyl-[acyl-carrier-protein] synthase 2. These proteins were modeled using AlphaFold2, validated through several structural analyses, and were subjected to molecular docking and ADMET analysis. Molecular dynamics simulations determined the stability of the ligand-target complexes, providing potential therapeutic options against Y. pestis.
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Affiliation(s)
- Lei Chen
- Jiangsu Vocational College of Medicine, Yancheng, China
- School of Graduate Studies, Management and Science University, Shah Alam, Malaysia
| | - Lihu Zhang
- Jiangsu Vocational College of Medicine, Yancheng, China
| | - Yanping Li
- Jiangsu Vocational College of Medicine, Yancheng, China
| | - Liang Qiao
- School of Environmental Science and Engineering, Yancheng Institute of Technology, Yancheng, China
| | - Suresh Kumar
- Faculty of Health and Life Sciences, Management and Science University, University Drive, Off Persiaran Olahraga, 40100, Shah Alam, Selangor, Malaysia.
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Nazir A, Ijaz M, Rehman HM, Sajjad M. Rigidifying Flexible Sites: A Promising Strategy to Improve Thermostability of Lysophospholipase From Pyrococcus abyssi. Proteins 2024. [PMID: 39291641 DOI: 10.1002/prot.26748] [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: 06/15/2024] [Revised: 08/22/2024] [Accepted: 08/30/2024] [Indexed: 09/19/2024]
Abstract
High thermostability of the enzymes is one of the distinguishing characteristics that increase their industrial utility. In the current research work, rigidifying the flexible amino acid residues of a lysophospholipase (Pa-LPL) from Pyrococcus abyssi was used as a protein engineering approach to improve its thermostability. A truncated variant of Pa-LPL (t-LPL∆12) was constructed by trimming its 12 amino acid residues (50-61) through overlap extension PCR. The truncated enzyme worked optimally at 65°C and pH 6.5 with remarkable thermostability at 65°C-85°C. In comparison to wild-type Pa-LPL, 5.8 and 1.2-fold increase in half-life (t1/2) of t-LPL∆12 was observed at 65 (optimum temperature) and 95°C, respectively. The activity of t-LPL∆12 was stimulated by 1 mM Cu2+ followed by Ca2+, Ni2+, Co2+, and Mg2+. Both substrate docking and experimental results indicated that the truncated enzyme could hydrolyze a variety of p-nitrophenyl esters. Km, Vmax, and Kcat for enzymatic hydrolysis of p-nitrophenyl butyrate were calculated to be 1 ± 0.087 mM, 1456 ± 36.474 U/mg, and 1.397 × 1011 min-1, respectively. In short, broad substrate specificity and thermostability of t-LPL∆12 are some of the distinctive features that make it an ideal candidate for degumming of vegetable oils.
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Affiliation(s)
- Arshia Nazir
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Maham Ijaz
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | | | - Muhammad Sajjad
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
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Kawka A, Nowak D, Koenig H, Pospieszny T. Exploring Triazole-Connected Steroid-Pyrimidine Hybrids: Synthesis, Spectroscopic Characterization, and Biological Assessment. ACS OMEGA 2024; 9:37995-38014. [PMID: 39281893 PMCID: PMC11391466 DOI: 10.1021/acsomega.4c04800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 08/16/2024] [Accepted: 08/22/2024] [Indexed: 09/18/2024]
Abstract
Molecules originating from natural sources are physicochemically and biologically diverse. The conjugation of two active biomolecules has become the foundation for medical and pharmaceutical sciences. An effective synthesis of 11 new steroid-pyrimidine conjugates containing 1,2,3-triazole rings was carried out. The group of 3α-OH bile acids (lithocholic, deoxycholic, cholic) and 3β-OH sterols (cholesterol, cholestanol) were respectively modified to azidoacetates. 2-thiouracil was converted into N(1)S and N(3)S dipropargyl derivatives. Azide-alkyne cycloaddition in the presence of copper(I) of the obtained compounds led to the preparation of 1,2,3-triazole derivatives. Based on a series of spectroscopic (1H NMR, 13C NMR, Fourier-transform infrared (FT-IR)), spectrometric analyses (Electrospray ionization-mass spectrometry (ESI-MS), electron impact-mass spectrometry (EI-MS)), and semiempirical calculations, the structures of all compounds were confirmed. In silico biological tests and molecular docking (for domain 1KZN, 2H94, 5V5Z, 1EZF, 2Q85) were performed for selected compounds. The tests performed indicate the theoretical antimicrobial potential of the obtained ligands.
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Affiliation(s)
- Anna Kawka
- Department of Bioactive Products, Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8 Street, 61-614 Poznań, Poland
| | - Damian Nowak
- Department of Quantum Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8 Street, 61-614 Poznań, Poland
| | - Hanna Koenig
- Department of Bioactive Products, Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8 Street, 61-614 Poznań, Poland
| | - Tomasz Pospieszny
- Department of Bioactive Products, Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8 Street, 61-614 Poznań, Poland
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Xu Y, Liang X, Hyun CG. Discovery of Indole-Thiourea Derivatives as Tyrosinase Inhibitors: Synthesis, Biological Evaluation, Kinetic Studies, and In Silico Analysis. Int J Mol Sci 2024; 25:9636. [PMID: 39273583 PMCID: PMC11394742 DOI: 10.3390/ijms25179636] [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: 07/29/2024] [Revised: 09/03/2024] [Accepted: 09/04/2024] [Indexed: 09/15/2024] Open
Abstract
Tyrosinase, a key enzyme in melanin synthesis, represents a crucial therapeutic target for hyperpigmentation disorders due to excessive melanin production. This study aimed to design and evaluate a series of indole-thiourea derivatives by conjugating thiosemicarbazones with strong tyrosinase inhibitory activity to indole. Among these derivatives, compound 4b demonstrated tyrosinase inhibitory activity with an IC50 of 5.9 ± 2.47 μM, outperforming kojic acid (IC50 = 16.4 ± 3.53 μM). Kinetic studies using Lineweaver-Burk plots confirmed competitive inhibition by compound 4b. Its favorable ADMET and drug-likeness properties make compound 4b a promising therapeutic candidate with a reduced risk of toxicity. Molecular docking revealed that the compounds bind strongly to mushroom tyrosinase (mTYR) and human tyrosinase-related protein 1 (TYRP1), with compound 4b showing superior binding energies of -7.0 kcal/mol (mTYR) and -6.5 kcal/mol (TYRP1), surpassing both kojic acid and tropolone. Molecular dynamics simulations demonstrated the stability of the mTYR-4b complex with low RMSD and RMSF and consistent Rg and SASA values. Persistent strong hydrogen bonds with mTYR, along with favorable Gibbs free energy and MM/PBSA calculations (-19.37 kcal/mol), further support stable protein-ligand interactions. Overall, compound 4b demonstrated strong tyrosinase inhibition and favorable pharmacokinetics, highlighting its potential for treating pigmentary disorders.
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Affiliation(s)
- Yang Xu
- Jeju Inside Agency and Cosmetic Science Center, Department of Chemistry and Cosmetics, Jeju National University, Jeju 63243, Republic of Korea
| | - Xuhui Liang
- Jeju Inside Agency and Cosmetic Science Center, Department of Chemistry and Cosmetics, Jeju National University, Jeju 63243, Republic of Korea
| | - Chang-Gu Hyun
- Jeju Inside Agency and Cosmetic Science Center, Department of Chemistry and Cosmetics, Jeju National University, Jeju 63243, Republic of Korea
- Department of Beauty and Cosmetology, Jeju National University, Jeju 63243, Republic of Korea
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Ismail EA, Omolo CA, Gafar MA, Khan R, Nyandoro VO, Yakubu ES, Mackraj I, Tageldin A, Govender T. Novel peptide and hyaluronic acid coated biomimetic liposomes for targeting bacterial infections and sepsis. Int J Pharm 2024; 662:124493. [PMID: 39048042 DOI: 10.1016/j.ijpharm.2024.124493] [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: 12/07/2023] [Revised: 07/12/2024] [Accepted: 07/17/2024] [Indexed: 07/27/2024]
Abstract
Sepsis is a life-threatening syndrome resulting from an imbalanced immune response to severe infections. Despite advances in nanomedicines, effective treatments for sepsis are still lacking. Herein, vancomycin free base (VCM)-loaded dual functionalized biomimetic liposomes based on a novel TLR4-targeting peptide (P3) and hyaluronic acid (HA) (HA-P3-Lipo) were developed to enhance sepsis therapy. The nanocarrier revealed appropriate physicochemical parameters, good stability, and biocompatibility. The release of VCM from HA-P3-Lipo was found to be sustained with 76 % VCM released in 48 h. The biomimicry was elucidated by in silico tools and MST and results confirmed strong binding between the system and TLR4. Furthermore, HA-P3-Lipo revealed 2-fold enhanced antibacterial activity against S. aureus, sustained antibacterial activity against MRSA over 72 h and 5-fold better MRSA biofilm inhibition compared to bare VCM. Bacterial-killing kinetics and flow cytometry confirmed the superiority of HA-P3-Lipo in eliminating MRSA faster than VCM. The in vivo potential of the nanocarrier was elucidated in an MRSA-induced sepsis mice model, and the results confirmed the superiority of HA-P3-Lipo compared to free VCM in eliminating bacteria and down-regulating the proinflammatory markers. Therefore, HA-P3-Lipo exhibits potential as a promising novel multi-functional nanosystem against sepsis and could significantly contribute to the transformation of sepsis therapy.
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Affiliation(s)
- Eman A Ismail
- Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban, South Africa; Department of Pharmaceutics, Faculty of Pharmacy, University of Gezira, Wad Medani, Sudan
| | - Calvin A Omolo
- Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban, South Africa; United States International University-Africa, School of Pharmacy and Health Sciences, Department of Pharmaceutics, P. O. Box 14634-00800, Nairobi, Kenya.
| | - Mohammed A Gafar
- Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban, South Africa
| | - Rene Khan
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Vincent O Nyandoro
- Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban, South Africa; School of Pharmacy, Kabarak University, P.O BOX Private bag 20157, Nakuru, Kenya
| | - Elliasu S Yakubu
- Biomedical Research and Innovation Platform (BRIP), South African Medical Research Council (SAMRC), Cape Town 7505, South Africa
| | - Irene Mackraj
- Discipline of Human Physiology, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Abdelrahman Tageldin
- Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban, South Africa
| | - Thirumala Govender
- Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban, South Africa.
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Alam MS, Sultana A, Kibria MK, Khanam A, Wang G, Mollah MNH. Identification of Hub of the Hub-Genes From Different Individual Studies for Early Diagnosis, Prognosis, and Therapies of Breast Cancer. Bioinform Biol Insights 2024; 18:11779322241272386. [PMID: 39239087 PMCID: PMC11375675 DOI: 10.1177/11779322241272386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 07/09/2024] [Indexed: 09/07/2024] Open
Abstract
Breast cancer (BC) is a complex disease, which causes of high mortality rate in women. Early diagnosis and therapeutic improvements may reduce the mortality rate. There were more than 74 individual studies that have suggested BC-causing hub-genes (HubGs) in the literature. However, we observed that their HubG sets are not so consistent with each other. It may be happened due to the regional and environmental variations with the sample units. Therefore, it was required to explore hub of the HubG (hHubG) sets that might be more representative for early diagnosis and therapies of BC in different country regions and their environments. In this study, we selected top-ranked 10 HubGs (CCNB1, CDK1, TOP2A, CCNA2, ESR1, EGFR, JUN, ACTB, TP53, and CCND1) as the hHubG set by the protein-protein interaction network analysis based on all of 74 individual HubG sets. The hHubG set enrichment analysis detected some crucial biological processes, molecular functions, and pathways that are significantly associated with BC progressions. The expression analysis of hHubGs by box plots in different stages of BC progression and BC prediction models indicated that the proposed hHubGs can be considered as the early diagnostic and prognostic biomarkers. Finally, we suggested hHubGs-guided top-ranked 10 candidate drug molecules (SORAFENIB, AMG-900, CHEMBL1765740, ENTRECTINIB, MK-6592, YM201636, masitinib, GSK2126458, TG-02, and PAZOPANIB) by molecular docking analysis for the treatment against BC. We investigated the stability of top-ranked 3 drug-target complexes (SORAFENIB vs ESR1, AMG-900 vs TOP2A, and CHEMBL1765740 vs EGFR) by computing their binding free energies based on 100-ns molecular dynamic (MD) simulation based Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) approach and found their stable performance. The literature review also supported our findings much more for BC compared with the results of individual studies. Therefore, the findings of this study may be useful resources for early diagnosis, prognosis, and therapies of BC.
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Affiliation(s)
- Md Shahin Alam
- Center of Translational Medicine, The First People's Hospital of Taicang, Taicang Affiliated Hospital of Soochow University, Suzhou, China
- Laboratory of Molecular Neuropathology, Department of Pharmacology, Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, China
- Bioinformatics Laboratory (Dry), Department of Statistics, University of Rajshahi, Rajshahi, Bangladesh
| | - Adiba Sultana
- Bioinformatics Laboratory (Dry), Department of Statistics, University of Rajshahi, Rajshahi, Bangladesh
- Medical Big Data Center, Guangdong Provincial People's Hospital/Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Md Kaderi Kibria
- Bioinformatics Laboratory (Dry), Department of Statistics, University of Rajshahi, Rajshahi, Bangladesh
| | - Alima Khanam
- Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi, Bangladesh
| | - Guanghui Wang
- Center of Translational Medicine, The First People's Hospital of Taicang, Taicang Affiliated Hospital of Soochow University, Suzhou, China
| | - Md Nurul Haque Mollah
- Bioinformatics Laboratory (Dry), Department of Statistics, University of Rajshahi, Rajshahi, Bangladesh
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Basak P, Dastidar DG, Ghosh D, Chakraborty T, Sau S, Chakrabarti G. Staphylococcus aureus major cell division protein FtsZ assembly is inhibited by silibinin, a natural flavonolignan that also blocked bacterial growth and biofilm formation. Int J Biol Macromol 2024; 279:135252. [PMID: 39222779 DOI: 10.1016/j.ijbiomac.2024.135252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 08/29/2024] [Accepted: 08/30/2024] [Indexed: 09/04/2024]
Abstract
The bacterial cell division protein FtsZ has been considered a potential therapeutic target due to its rapid treadmilling that induces cellular wall construction in bacteria. The current study discovered a novel antimicrobial compound, silibinin, a natural flavonolignan and its impact on the recombinant S. aureus FtsZ (SaFtsZ). Silibinin inhibited S. aureus Newman growth in a dose-dependent manner. The IC50 and MIC values for silibinin were 75 μM and 200 μM, respectively. It had no cytotoxicity against HEK293 cells in vitro. Silibinin also enlarged the bacterial cell morphology by ∼40 folds and showed antibiofilm property. It perturbed the S. aureus membrane potential both at IC50 conc. and at MIC conc. Further, it inhibited both the polymerization and GTPase activity of SaFtsZ. It did not inhibit tubulin assembly, a eukaryotic FtsZ homolog. A fluorescence quenching study yielded the Kd value for SaFtsZ-Silibinin interaction and binding stoichiometry 0.857 ± 0.188 μM and 1:1, respectively. Both in silico study and competition assay indicated that silibinin binds at the GTP binding site on SaFtsZ. The Ki value for the silibinin-mediated inhibition of SaFtsZ was 8.8 μM. Therefore, these findings have comprehensively shown the antimicrobial behavior of silibinin on S. aureus Newman cells targeting SaFtsZ.
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Affiliation(s)
- Prithvi Basak
- Department of Biotechnology, Dr. B. C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, WB 700 019, India
| | - Debabrata Ghosh Dastidar
- Guru Nanak Institute of Pharmaceutical Science & Technology, 157/F Nilgunj Road, Panihati, Kolkata 700114, West Bengal, India
| | - Dipanjan Ghosh
- Department of Biotechnology, Dr. B. C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, WB 700 019, India
| | - Tushar Chakraborty
- Department of Biological Sciences, Bose Institute, Kolkata 700091, West Bengal, India
| | - Subrata Sau
- Department of Biological Sciences, Bose Institute, Kolkata 700091, West Bengal, India
| | - Gopal Chakrabarti
- Department of Biotechnology, Dr. B. C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, WB 700 019, India.
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Chikhale RV, Pawar SP, Kolpe MS, Shinde OD, Dahlous KA, Mohammad S, Patil PC, Bhowmick S. Identification of mycobacterial Thymidylate kinase inhibitors: a comprehensive pharmacophore, machine learning, molecular docking, and molecular dynamics simulation studies. Mol Divers 2024:10.1007/s11030-024-10967-w. [PMID: 39152354 DOI: 10.1007/s11030-024-10967-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Accepted: 08/08/2024] [Indexed: 08/19/2024]
Abstract
Thymidylate kinase (TMK) is a pivotal enzyme in Mycobacterium tuberculosis (Mtb), crucial for phosphorylating thymidine monophosphate (dTMP) to thymidine diphosphate (dTDP), thereby playing a critical role in DNA biosynthesis. Dysregulation or inhibition of TMK activity disrupts DNA replication and cell division, making it an attractive target for anti-tuberculosis drug development. In this study, the statistically validated pharmacophore mode was developed from a set of known TMK inhibitors. Further, the robust pharmacophore was considered for screening the Enamine database. The chemical space was reduced through multiple molecular docking approaches, pharmacokinetics, and absolute binding energy estimation. Two different molecular docking algorithms favor the strong binding affinity of the proposed molecules towards TMK. Machine learning-based absolute binding energy also showed the potentiality of the proposed molecules. The binding interactions analysis exposed the strong binding affinity between the proposed molecules and active site amino residues of TMK. Several statistical parameters from all atoms MD simulation explained the stability between proposed molecules and TMK in the dynamic states. The MM-GBSA approach also found a strong binding affinity for each proposed molecule. Therefore, the proposed molecules might be crucial TMK inhibitors for managing Mtb inhibition subjected to in vitro/in vivo validations.
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Affiliation(s)
- Rupesh V Chikhale
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College London, London, UK.
| | - Surbhi Pravin Pawar
- SilicoScientia Private Limited, Nagananda Commercial Complex, No. 07/3, 15/1, 18th Main Road, Jayanagar 9th Block, Bengaluru, 560041, India
- Department of Bioinformatics, Rajiv Gandhi Institute of IT and Biotechnology, Bharati Vidyapeeth (Deemed to be University), Pune-Satara Road, Pune, India
| | - Mahima Sudhir Kolpe
- SilicoScientia Private Limited, Nagananda Commercial Complex, No. 07/3, 15/1, 18th Main Road, Jayanagar 9th Block, Bengaluru, 560041, India
| | - Omkar Dilip Shinde
- SilicoScientia Private Limited, Nagananda Commercial Complex, No. 07/3, 15/1, 18th Main Road, Jayanagar 9th Block, Bengaluru, 560041, India
- Department of Bioinformatics, Rajiv Gandhi Institute of IT and Biotechnology, Bharati Vidyapeeth (Deemed to be University), Pune-Satara Road, Pune, India
| | - Kholood A Dahlous
- Department of Chemistry, College of Science, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Saikh Mohammad
- Department of Chemistry, College of Science, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Pritee Chunarkar Patil
- Department of Bioinformatics, Rajiv Gandhi Institute of IT and Biotechnology, Bharati Vidyapeeth (Deemed to be University), Pune-Satara Road, Pune, India
| | - Shovonlal Bhowmick
- SilicoScientia Private Limited, Nagananda Commercial Complex, No. 07/3, 15/1, 18th Main Road, Jayanagar 9th Block, Bengaluru, 560041, India
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Arbi M, Khedhiri M, Ayouni K, Souiai O, Dhouib S, Ghanmi N, Benkahla A, Triki H, Haddad-Boubaker S. Recombination Events Among SARS-CoV-2 Omicron Subvariants: Impact on Spike Interaction With ACE2 Receptor and Neutralizing Antibodies. Evol Bioinform Online 2024; 20:11769343241272415. [PMID: 39149136 PMCID: PMC11325312 DOI: 10.1177/11769343241272415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 07/03/2024] [Indexed: 08/17/2024] Open
Abstract
The recombination plays a key role in promoting evolution of RNA viruses and emergence of potentially epidemic variants. Some studies investigated the recombination occurrence among SARS-CoV-2, without exploring its impact on virus-host interaction. In the aim to investigate the burden of recombination in terms of frequency and distribution, the occurrence of recombination was first explored in 44 230 Omicron sequences among BQ subvariants and the under investigation "ML" (Multiple Lineages) denoted sequences, using 3seq software. Second, the recombination impact on interaction between the Spike protein and ACE2 receptor as well as neutralizing antibodies (nAbs), was analyzed using docking tools. Recombination was detected in 56.91% and 82.20% of BQ and ML strains, respectively. It took place mainly in spike and ORF1a genes. For BQ recombinant strains, the docking analysis showed that the spike interacted strongly with ACE2 and weakly with nAbs. The mutations S373P, S375F and T376A constitute a residue network that enhances the RBD interaction with ACE2. Thirteen mutations in RBD (S373P, S375F, T376A, D405N, R408S, K417N, N440K, S477N, P494S, Q498R, N501Y, and Y505H) and NTD (Y240H) seem to be implicated in immune evasion of recombinants by altering spike interaction with nAbs. In conclusion, this "in silico" study demonstrated that the recombination mechanism is frequent among Omicron BQ and ML variants. It highlights new key mutations, that potentially implicated in enhancement of spike binding to ACE2 (F376A) and escape from nAbs (RBD: F376A, D405N, R408S, N440K, S477N, P494S, and Y505H; NTD: Y240H). Our findings present considerable insights for the elaboration of effective prophylaxis and therapeutic strategies against future SARS-CoV-2 waves.
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Affiliation(s)
- Marwa Arbi
- Laboratory of Bioinformatics, Biomathematics and Biostatistics (BIMS), Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Marwa Khedhiri
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia
- Research Laboratory: "Virus, Vector and Host" (LR20IPT02), Pasteur Institute of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Clinical Investigation Center (CIC), Pasteur Institute of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Kaouther Ayouni
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia
- Research Laboratory: "Virus, Vector and Host" (LR20IPT02), Pasteur Institute of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Clinical Investigation Center (CIC), Pasteur Institute of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Oussema Souiai
- Laboratory of Bioinformatics, Biomathematics and Biostatistics (BIMS), Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia
- Higher Institute of Medical Technologies of Tunis, Tunis Al Manar University, Tunis, Tunisia
| | - Samar Dhouib
- High School of Statistics and Analysis of Information (ESSAI), University of Carthage, Tunis, Tunisia
| | - Nidhal Ghanmi
- Laboratory of Bioinformatics, Biomathematics and Biostatistics (BIMS), Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Alia Benkahla
- Laboratory of Bioinformatics, Biomathematics and Biostatistics (BIMS), Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Henda Triki
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia
- Research Laboratory: "Virus, Vector and Host" (LR20IPT02), Pasteur Institute of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Clinical Investigation Center (CIC), Pasteur Institute of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Sondes Haddad-Boubaker
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia
- Research Laboratory: "Virus, Vector and Host" (LR20IPT02), Pasteur Institute of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Clinical Investigation Center (CIC), Pasteur Institute of Tunis, University of Tunis El Manar, Tunis, Tunisia
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Wu JW, Gao W, Shen LP, Chen YL, Du SQ, Du ZY, Zhao XD, Lu XJ. Leonurus japonicus Houtt. modulates neuronal apoptosis in intracerebral hemorrhage: Insights from network pharmacology and molecular docking. JOURNAL OF ETHNOPHARMACOLOGY 2024; 330:118223. [PMID: 38642624 DOI: 10.1016/j.jep.2024.118223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 04/09/2024] [Accepted: 04/17/2024] [Indexed: 04/22/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Leonurus japonicus Houtt. (Labiatae), commonly known as Chinese motherwort, is a herbaceous flowering plant that is native to Asia. It is widely acknowledged in traditional medicine for its diuretic, hypoglycemic, antiepileptic properties and neuroprotection. Currently, Leonurus japonicus (Leo) is included in the Pharmacopoeia of the People's Republic of China. Traditional Chinese Medicine (TCM) recognizes Leo for its myriad pharmacological attributes, but its efficacy against ICH-induced neuronal apoptosis is unclear. AIMS OF THE STUDY This study aimed to identify the potential targets and regulatory mechanisms of Leo in alleviating neuronal apoptosis after ICH. MATERIALS AND METHODS The study employed network pharmacology, UPLC-Q-TOF-MS technique, molecular docking, pharmacodynamic studies, western blotting, and immunofluorescence techniques to explore its potential mechanisms. RESULTS Leo was found to assist hematoma absorption, thus improving the neurological outlook in an ICH mouse model. Importantly, molecular docking highlighted JAK as Leo's potential therapeutic target in ICH scenarios. Further experimental evidence demonstrated that Leo adjusts JAK1 and STAT1 phosphorylation, curbing Bax while augmenting Bcl-2 expression. CONCLUSION Leo showcases potential in mitigating neuronal apoptosis post-ICH, predominantly via the JAK/STAT mechanism.
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Affiliation(s)
- Jia-Wei Wu
- Neuroscience Center, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu Province, 214122, PR China; Department of Neurosurgery, Jiangnan University Medical Center, Wuxi, Jiangsu Province, 214122, PR China; Wuxi Neurosurgical Institute, Wuxi, Jiangsu Province, 214122, PR China
| | - Wei Gao
- Department of Neurology, Wuxi Ninth People's Hospital Affiliated to Soochow University, Wuxi, Jiangsu Province, 214122, PR China
| | - Li-Ping Shen
- Department of Neurosurgery, Jiangnan University Medical Center, Wuxi, Jiangsu Province, 214122, PR China; Wuxi Neurosurgical Institute, Wuxi, Jiangsu Province, 214122, PR China
| | - Yong-Lin Chen
- Neuroscience Center, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu Province, 214122, PR China; Department of Neurosurgery, Jiangnan University Medical Center, Wuxi, Jiangsu Province, 214122, PR China; Wuxi Neurosurgical Institute, Wuxi, Jiangsu Province, 214122, PR China
| | - Shi-Qing Du
- Neuroscience Center, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu Province, 214122, PR China; Department of Neurosurgery, Jiangnan University Medical Center, Wuxi, Jiangsu Province, 214122, PR China; Wuxi Neurosurgical Institute, Wuxi, Jiangsu Province, 214122, PR China
| | - Zhi-Yong Du
- Neuroscience Center, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu Province, 214122, PR China; Department of Neurosurgery, Jiangnan University Medical Center, Wuxi, Jiangsu Province, 214122, PR China; Wuxi Neurosurgical Institute, Wuxi, Jiangsu Province, 214122, PR China
| | - Xu-Dong Zhao
- Neuroscience Center, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu Province, 214122, PR China; Department of Neurosurgery, Jiangnan University Medical Center, Wuxi, Jiangsu Province, 214122, PR China; Wuxi Neurosurgical Institute, Wuxi, Jiangsu Province, 214122, PR China.
| | - Xiao-Jie Lu
- Neuroscience Center, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu Province, 214122, PR China; Department of Neurosurgery, Jiangnan University Medical Center, Wuxi, Jiangsu Province, 214122, PR China; Wuxi Neurosurgical Institute, Wuxi, Jiangsu Province, 214122, PR China.
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Campos-Fernández E, Alqualo NO, Vaz ER, Rodrigues CM, Alonso-Goulart V. Unveiling the characteristics of D4 and R4 aptamers for their future use in prostate cancer clinical practice. Biophys Chem 2024; 311:107259. [PMID: 38763045 DOI: 10.1016/j.bpc.2024.107259] [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: 02/25/2024] [Revised: 04/24/2024] [Accepted: 05/12/2024] [Indexed: 05/21/2024]
Abstract
The DNA and RNA aptamers D4 and R4, respectively, emerged from the modification of PC-3 cell-binding aptamer A4. Our objective was to characterize the aptamers in silico and in vitro and begin to identify their target molecules. We represented their structures using computational algorithms; evaluated their binding to several prostate cell lines and their effects on the viability and migration of these cells; and determined their dissociation constant by flow cytometry. We analyzed circulating prostate tumor cells from patients using D4, R4, anti-CD133 and anti-CD44. Finally, the target proteins of both aptamers were precipitated and identified by mass spectrometry to simulate their in silico docking. The aptamers presented similar structures and bound to prostate tumor cells without modifying the cellular parameters studied, but with different affinities. The ligand cells for both aptamers were CD44+, indicating that they could identify cells in the mesenchymal stage of the metastatic process. The possible target proteins NXPE1, ADAM30, and MUC6 need to be further studied to better understand their interaction with the aptamers. These results support the development of new assays to determine the clinical applications of D4 and R4 aptamers in prostate cancer.
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Affiliation(s)
- Esther Campos-Fernández
- Laboratory of Nanobiotechnology Prof. Dr. Luiz Ricardo Goulart Filho, Institute of Biotechnology, Universidade Federal de Uberlândia, Uberlândia, MG, Brazil
| | - Nathalia Oliveira Alqualo
- Laboratory of Nanobiotechnology Prof. Dr. Luiz Ricardo Goulart Filho, Institute of Biotechnology, Universidade Federal de Uberlândia, Uberlândia, MG, Brazil
| | - Emília Rezende Vaz
- Laboratory of Nanobiotechnology Prof. Dr. Luiz Ricardo Goulart Filho, Institute of Biotechnology, Universidade Federal de Uberlândia, Uberlândia, MG, Brazil
| | - Cláudia Mendonça Rodrigues
- Laboratory of Nanobiotechnology Prof. Dr. Luiz Ricardo Goulart Filho, Institute of Biotechnology, Universidade Federal de Uberlândia, Uberlândia, MG, Brazil
| | - Vivian Alonso-Goulart
- Laboratory of Nanobiotechnology Prof. Dr. Luiz Ricardo Goulart Filho, Institute of Biotechnology, Universidade Federal de Uberlândia, Uberlândia, MG, Brazil.
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15
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Subin JA, Shrestha RLS. Computational Assessment of the Phytochemicals of Panax ginseng C.A. Meyer Against Dopamine Receptor D1 for Early Huntington's Disease Prophylactics. Cell Biochem Biophys 2024:10.1007/s12013-024-01426-2. [PMID: 39046621 DOI: 10.1007/s12013-024-01426-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2024] [Indexed: 07/25/2024]
Abstract
A herb, Panax ginseng C.A. Meyer has been used traditionally for the treatment of various diseases. In this work, its chemical components have been explored by computational methods for the possibility of therapeutic potential against early Huntington's disease. The molecular docking calculations against dopamine receptor D1 (PDB ID: 7X2F) involved in pathogenesis of early Huntington's disease gave the binding affinities (kcal/mol) of schizandrin (-10.530), ergosterol (-10.124), protopanaxadiol (-9.650), panaxydol (-9.399), diphenhydramine (-9.358), and panasenoside (-9.358). The values for native ligand (-7.748) and some selected drugs, Nefazodone (-9.880), Risperidone (-9.752), and Haloperidol (-9.712) were higher revealing weaker interactions. The stability assessment of top protein-ligand adducts in terms of various geometrical and thermodynamical parameters extracted from 200 ns molecular dynamics simulations pointed to schizandrin, protopanaxadiol, and panasenoside as hit molecules. The minimal translational and rotational motion of the docked ligands at orthosteric pocket of the receptor at near physiological conditions hinted at the probability of it restricting or inhibiting over-activation of DRD1. The sustained thermodynamic spontaneity of complex formation reaction augmented the inferences derived from spatial results. The phytochemicals from Panax ginseng could be used in the prophylactics of early Huntington's disease and recommendation is made for further evaluation by experimental work.
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Affiliation(s)
- Jhashanath Adhikari Subin
- Bioinformatics and Cheminformatics Division, Scientific Research and Training Nepal P. Ltd., Kaushaltar, Bhaktapur, 44800, Nepal
| | - Ram Lal Swagat Shrestha
- Bioinformatics and Cheminformatics Division, Scientific Research and Training Nepal P. Ltd., Kaushaltar, Bhaktapur, 44800, Nepal.
- Department of Chemistry, Amrit Campus, Tribhuvan University, Thamel, Kathmandu, 44600, Nepal.
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16
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Putri AF, Utomo DH, Tunjung WAS, Putri WA. Analysis of the anti-Alzheimer potential of bioactive compounds from Citrus hystrix DC. peel, leaf, and essential oil by network pharmacology. Heliyon 2024; 10:e33496. [PMID: 39050443 PMCID: PMC11267028 DOI: 10.1016/j.heliyon.2024.e33496] [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: 02/21/2024] [Revised: 05/30/2024] [Accepted: 06/21/2024] [Indexed: 07/27/2024] Open
Abstract
Alzheimer's disease (AD) is the most known neurodegenerative disease, and its prevalence is predicted to increase significantly. Discovering novel drugs and treatments for AD is urgently needed. Drugs from natural products have been preferred lately due to their high potential and low toxicity. Citrus hystrix DC. (kaffir lime; KL) is one such herbal plant that is found abundantly in Southeast Asia with many biological activities. In this study, the potential of bioactive compounds from KL peel, leaf, and essential oil as anti-AD agents was explored using network pharmacology. First, the compounds were identified with KNApSAcK database and related literature. Subsequently, the targets of each corresponding compound were determined with SEA Search Server and Swiss Target Prediction, while the proteins associated with AD were identified using OMIM, GenCLiP3, and DisGeNET. Furthermore, a protein-protein interaction network and a compound-target interaction network were constructed to identify the most crucial proteins and compounds in the network by employing Cytoscape v3.9.1. The study continued with pathway enrichment analysis using STRING v1.7.1, molecular docking with PyRx and SwissDock, and molecular dynamics simulation with YASARA for further confirmation. Our results showed that almost all the secondary metabolites of KL targeted AD-associated genes, with oxypeucedanin and citrusoside A showing the highest anti-AD potential and targeting essential genes, EGFR and MAPK14, respectively. These targets were associated with inflammatory and oxidative stress pathways, indicating the potential mechanism of KL in attenuating AD clinical manifestation.
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Affiliation(s)
- Adhisa Fathirisari Putri
- Faculty of Biology, Universitas Gadjah Mada, Jl. Teknika Selatan, Sekip Utara, Yogyakarta, 55281, Indonesia
- Bioinformatics Research Center, INBIO-Indonesia, Malang, 65162, Indonesia
| | - Didik Huswo Utomo
- Bioinformatics Research Center, INBIO-Indonesia, Malang, 65162, Indonesia
- Biosystem Education Center, Brawijaya University, Malang, 65145, Indonesia
| | - Woro Anindito Sri Tunjung
- Faculty of Biology, Universitas Gadjah Mada, Jl. Teknika Selatan, Sekip Utara, Yogyakarta, 55281, Indonesia
| | - Wahyu Aristyaning Putri
- Faculty of Biology, Universitas Gadjah Mada, Jl. Teknika Selatan, Sekip Utara, Yogyakarta, 55281, Indonesia
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17
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El-Khamisi EF, Soliman EAM, El-Sayed GM, Nour SA, Abdel-Monem MO, Hassan MG. Optimization, gene cloning, expression, and molecular docking insights for enhanced cellulase enzyme production by Bacillus amyloliquefaciens strain elh1. Microb Cell Fact 2024; 23:191. [PMID: 38956640 PMCID: PMC11218070 DOI: 10.1186/s12934-024-02454-6] [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: 03/21/2024] [Accepted: 06/07/2024] [Indexed: 07/04/2024] Open
Abstract
BACKGROUND In this study, we isolated a cellulase-producing bacterium, Bacillus amyloliquefaciens strain elh, from rice peel. We employed two optimization methods to enhance the yield of cellulase. Firstly, we utilized a one-variable-at-a-time (OVAT) approach to evaluate the impact of individual physical and chemical parameters. Subsequently, we employed response surface methodology (RSM) to investigate the interactions among these factors. We heterologously expressed the cellulase encoding gene using a cloning vectorin E. coli DH5α. Moreover, we conducted in silico molecular docking analysis to analyze the interaction between cellulase and carboxymethyl cellulose as a substrate. RESULTS The bacterial isolate eh1 exhibited an initial cellulase activity of 0.141 ± 0.077 U/ml when cultured in a specific medium, namely Basic Liquid Media (BLM), with rice peel as a substrate. This strain was identified as Bacillus amyloliquefaciens strain elh1 through 16S rRNA sequencing, assigned the accession number OR920278 in GenBank. The optimal incubation time was found to be 72 h of fermentation. Urea was identified as the most suitable nitrogen source, and dextrose as the optimal sugar, resulting in a production increase to 5.04 ± 0.120 U/ml. The peak activity of cellulase reached 14.04 ± 0.42 U/ml utilizing statistical optimization using Response Surface Methodology (RSM). This process comprised an initial screening utilizing the Plackett-Burman design and further refinement employing the BOX -Behnken Design. The gene responsible for cellulase production, egl, was effectively cloned and expressed in E. coli DH5α. The transformed cells exhibited a cellulase activity of 22.3 ± 0.24 U/ml. The egl gene sequence was deposited in GenBank with the accession number PP194445. In silico molecular docking revealed that the two hydroxyl groups of carboxymethyl cellulose bind to the residues of Glu169 inside the binding pocket of the CMCase. This interaction forms two hydrogen bonds, with an affinity score of -5.71. CONCLUSIONS Optimization of cultural conditions significantly enhances the yield of cellulase enzyme when compared to unoptimized culturing conditions. Additionally, heterologous expression of egl gene showed that the recombinant form of the cellulase is active and that a valid expression system can contribute to a better yield of the enzyme.
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Affiliation(s)
- Elham F El-Khamisi
- Microbial Genetics Department, Biotechnology Research Institute, National Research Centre, 33 El-Bohouth St., (Former El-Tahrir St.) Dokki, P.O. 12622, Giza, Egypt
| | - Effat A M Soliman
- Microbial Genetics Department, Biotechnology Research Institute, National Research Centre, 33 El-Bohouth St., (Former El-Tahrir St.) Dokki, P.O. 12622, Giza, Egypt
| | - Ghada M El-Sayed
- Microbial Genetics Department, Biotechnology Research Institute, National Research Centre, 33 El-Bohouth St., (Former El-Tahrir St.) Dokki, P.O. 12622, Giza, Egypt
| | - Shaimaa A Nour
- Chemistry of Natural and Microbial Products Department, Pharmaceutical and Drug Industries Research Institute, National Research Centre, 33 El-Bohouth St., Dokki, P.O. 12622, Giza, Egypt.
| | - Mohamed O Abdel-Monem
- Botany and Microbiology Department, Faculty of Science, Benha University, Benha, 13511, Egypt
| | - Mervat G Hassan
- Botany and Microbiology Department, Faculty of Science, Benha University, Benha, 13511, Egypt
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18
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Ajiboye AT, Asekun OT, Ayipo YO, Mordi MN, Familoni OB, Ali Z, Khan IA. Phytochemicals and enzymes inhibitory potentials of leaves and rootbarks of Sarcocephallus latifolius (smith): In vitro and in silico investigations. Fitoterapia 2024; 176:106037. [PMID: 38801897 DOI: 10.1016/j.fitote.2024.106037] [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: 02/05/2024] [Revised: 05/17/2024] [Accepted: 05/24/2024] [Indexed: 05/29/2024]
Abstract
In this study, bioactive compounds were isolated and characterized from the leaves and root-barks extracts of S.latifolius, with subsequent in vitro experimental investigations for antihyperglycemic potentials on α-amylase and α-glucosidase enzymes. Thirteen bioactive compounds were identified, including 10-Hydroxystrictosamide (2) and Quinovic acid-3-O-α-L-rhamnosyl-28-O-β-d-glucopyranosyl ester (8), using chromatographic, nuclear magnetic resonance spectroscopy (NMR), and mass spectrometry (MS) techniques. Experimental assays revealed that compounds 1-4 exhibited potent inhibition of α-amylase and α-glucosidase, with compound 2 demonstrating the most potent α-amylase inhibition (IC50 value of 0.52 ± 0.003 μg/mL). Compound 8 showed a lower IC50 value (0.098 ± 0.016 μg/mL) against α-glucosidase compared to compound 2 and acarbose. Synergistic effects among the compounds could enhance their inhibitory actions on the enzymes, positioning them as potential anti-hyperglycemia agents. Compound 2 displayed the highest binding affinity (-7.970 kcal/mol) when docked against α-amylase (PDB ID: 2QV4), comparable to acarbose (-8.515 kcal/mol). It also ranked among the top ligands against α-glucosidase (PDB ID 3TOP), although compound 13 and acarbose had higher docking scores. All compounds exhibited ideal ADMET properties, suggesting good bioavailability and low toxicity. In conclusion, the isolated compounds exhibit promising antihyperglycemic potential and favourable safety profiles for further exploration.
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Affiliation(s)
- Abdulfatai Temitope Ajiboye
- Department of Chemistry and Industrial Chemistry, Faculty of Pure and Applied Sciences, PMB 1530, Kwara State University, Malete, Nigeria; Department of Chemistry, Faculty of Science, University of Lagos, Nigeria; National Center for Natural Products Research, School of Pharmacy, University of Mississippi, University, MS 38677, United States.
| | | | - Yusuf Oloruntoyin Ayipo
- Department of Chemistry and Industrial Chemistry, Faculty of Pure and Applied Sciences, PMB 1530, Kwara State University, Malete, Nigeria; Centre for Drug Research, Universiti Sains Malaysia, USM, 11800, Pulau Pinang, Malaysia
| | - Mohd Nizam Mordi
- Centre for Drug Research, Universiti Sains Malaysia, USM, 11800, Pulau Pinang, Malaysia
| | | | - Zulfiqar Ali
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, University, MS 38677, United States
| | - Ikhlas A Khan
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, University, MS 38677, United States
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19
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Sandhu G, Agrawal P, Bose S, Thelma BK. Building polarization into protein-inhibitor binding dynamics in rational drug design for rheumatoid arthritis. J Biomol Struct Dyn 2024; 42:5912-5930. [PMID: 37378542 DOI: 10.1080/07391102.2023.2229449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 06/20/2023] [Indexed: 06/29/2023]
Abstract
Standard force field-based simulations to accomplish structure-based evaluations of lead molecules is a powerful tool. Combining protein fragmentation into tractable sub-systems with continuum solvation method is envisaged to enable quantum mechanics-based electronic structure calculations of macromolecules in their realistic environment. This along with incorporation of many-body polarization effect in molecular dynamics simulations may augment an accurate description of electrostatics of protein-inhibitor systems for effective drug design. Rheumatoid arthritis (RA) is a complex autoimmune disorder plagued by the ceiling effect of current targeted therapies, encouraging identification of new druggable targets and corresponding drug design to tackle the refractory form of disease. In this study, polarization-inclusive force field approach has been used to model protein solvation and ligand binding for 'Mitogen-activated protein kinase' (MAP3K8), a regulatory node of notable pharmacological relevance in RA synovial biology. For MAP3K8 inhibitors belonging to different scaffold series, the calculations illustrated differential electrostatic contribution to their relative binding affinities and successfully explained examples from available structure-activity relationship studies. Results from this study exemplified i) the advantage of this approach in reliably ranking inhibitors having close nanomolar range activities for the same target; and ii) its prospective application in lead molecule identification aiding drug discovery efforts in RA.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Gurvisha Sandhu
- Department of Genetics, University of Delhi South Campus, New Delhi, Delhi, India
| | - Praveen Agrawal
- LeadInvent Technologies Private Limited, Biotech Centre, University of Delhi South Campus, New Delhi, Delhi, India
| | - Surojit Bose
- LeadInvent Technologies Private Limited, Biotech Centre, University of Delhi South Campus, New Delhi, Delhi, India
| | - B K Thelma
- Department of Genetics, University of Delhi South Campus, New Delhi, Delhi, India
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20
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Mosavi SZ, Colagar AH, Zahedi T, Seyedalipour B. 1,4-Diol Hq (TBHQ) vs 1,4-dithiol (TBDT); simulation of safe antioxidant with a lower carcinogenic activity. Sci Prog 2024; 107:368504241280869. [PMID: 39314158 DOI: 10.1177/00368504241280869] [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] [Indexed: 09/25/2024]
Abstract
OBJECTIVES tert-Butylhydroquinone (TBHQ) is an antioxidant and preservative used in unsaturated vegetable oils and processed foods. However, when consumed in higher doses daily, it may pose a threat to public health by potentially increasing the risk of cancer, as it has an affinity with both the aryl hydrocarbon receptor (AhR) and the estrogen receptor alpha (ERα). METHODS This study aimed to examine the impact of substituting the 1,4-diol of TBHQ with 1,4-dithiol, referred to as TBDT, on the carcinogenic and antioxidant systems using computational methods. The binding affinity of TBHQ and TBDT to the two carcinogenic receptors, AhR and ERα, as well as to the antioxidant receptor Keap1 alone and in connection with Nrf2 (Nrf2-Keap1) was investigated through docking analysis. RESULTS The results indicated a decrease in TBDT's binding strength to ERα and AhR when assessed using Molegro Virtual Docker (P-value: 0.0001 and 0.00001, respectively), AutoDock Vina (P-value: 0.0001 and 0.0001), and the online server Fast DRH (P-value: 0.0001 and 0.0001). However, TBDT's binding affinity to Keap1 was predicted to be significantly stronger than TBHQ's by both MVD and AutoDock Vina (P-value: 0.0001 and 0.04), while its binding to Nrf2-Keap1 assessed to be stronger only by MVD (P-value: 0.0001). CONCLUSION These findings suggest that TBDT not only exhibits higher antioxidant activity as a better ligand for the antioxidant system but also shows lower affinity with the AhR and ERα receptors. Therefore, TBDT can be considered a safer compound than TBHQ.
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Affiliation(s)
- Seyed Zahra Mosavi
- Department of Molecular and Cell Biology, Faculty of Science, University of Mazandaran, Babolsar, Mazandaran, Iran
| | - Abasalt Hosseinzadeh Colagar
- Department of Molecular and Cell Biology, Faculty of Science, University of Mazandaran, Babolsar, Mazandaran, Iran
| | - Tahereh Zahedi
- Department of Molecular and Cell Biology, Faculty of Science, University of Mazandaran, Babolsar, Mazandaran, Iran
| | - Bagher Seyedalipour
- Department of Molecular and Cell Biology, Faculty of Science, University of Mazandaran, Babolsar, Mazandaran, Iran
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21
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Rathod S, Dey S, Pawar S, Dhavale R, Choudhari P, Rajakumara E, Mahuli D, Bhagwat D, Tamboli Y, Sankpal P, Mali S, More H. Identification of potential biogenic chalcones against antibiotic resistant efflux pump (AcrB) via computational study. J Biomol Struct Dyn 2024; 42:5178-5196. [PMID: 37340697 DOI: 10.1080/07391102.2023.2225099] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 06/09/2023] [Indexed: 06/22/2023]
Abstract
The cases of bacterial multidrug resistance are increasing every year and becoming a serious concern for human health. Multidrug efflux pumps are key players in the formation of antibiotic resistance, which transfer out a broad spectrum of drugs from the cell and convey resistance to the host. Efflux pumps have significantly reduced the efficacy of the previously available antibiotic armory, thereby increasing the frequency of therapeutic failures. In gram-negative bacteria, the AcrAB-TolC efflux pump is the principal transporter of the substrate and plays a major role in the formation of antibiotic resistance. In the current work, advanced computer-aided drug discovery approaches were utilized to find hit molecules from the library of biogenic chalcones against the bacterial AcrB efflux pump. The results of the performed computational studies via molecular docking, drug-likeness prediction, pharmacokinetic profiling, pharmacophore mapping, density functional theory, and molecular dynamics simulation study provided ZINC000004695648, ZINC000014762506, ZINC000014762510, ZINC000095099506, and ZINC000085510993 as stable hit molecules against the AcrB efflux pumps. Identified hits could successfully act against AcrB efflux pumps after optimization as lead molecules.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sanket Rathod
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, MS, India
| | - Sreenath Dey
- Department of Biotechnology, Indian Institute of Technology, Hyderabad, Kandi, Sangareddy, Telangana, India
| | - Swaranjali Pawar
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, MS, India
| | - Rakesh Dhavale
- Department of Pharmaceutics, Bharati Vidyapeeth College of Pharmacy, Kolhapur, MS, India
| | - Prafulla Choudhari
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, MS, India
| | - Eerappa Rajakumara
- Department of Biotechnology, Indian Institute of Technology, Hyderabad, Kandi, Sangareddy, Telangana, India
| | - Deepak Mahuli
- Department of Pharmacology, Bharati Vidyapeeth College of Pharmacy, Kolhapur, MS, India
| | - Durgacharan Bhagwat
- Department of Pharmaceutics, Bharati Vidyapeeth College of Pharmacy, Kolhapur, MS, India
| | - Yasinalli Tamboli
- King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard-Health Affairs, Riyadh, Saudi Arabia
| | - Poournima Sankpal
- Department of Pharmaceutical Chemistry, Ashokrao Mane College of Pharmacy, Kolhapur, MS, India
| | - Sachin Mali
- Department of Pharmaceutics, Y. D. Mane College of Pharmacy, Kagal, MS, India Kolhapur
| | - Harinath More
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, MS, India
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22
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Natu K, Dutta S, Bose K. cFLIP - An interacting partner and a novel substrate for pro-apoptotic serine protease HtrA2. Biochem Biophys Rep 2024; 38:101682. [PMID: 38511187 PMCID: PMC10950699 DOI: 10.1016/j.bbrep.2024.101682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 02/29/2024] [Accepted: 02/29/2024] [Indexed: 03/22/2024] Open
Abstract
Background HtrA2, a pro-apoptotic protease, plays a crucial role in apoptosis by cleaving inhibitory and anti-apoptotic proteins by translocating from mitochondria to the cytosol. Prior studies in ischemic cells have indicated that cytosolic HtrA2 triggers cFLIP degradation, plausibly through direct interaction. In this study, we have characterized the cFLIP protein, validated its interaction with HtrA2, and demonstrated that cFLIP is also a substrate of HtrA2. Methods We have identified the probable cleavage sites of cFLIP through gel-based assays and mass spectrometric analysis of the cleaved fragments. Results Our findings shed light on a key protein-protein interaction involving pro-apoptotic HtrA2, confirming cFLIP as its interacting partner and substrate. Conclusion Understanding the nuances of HtrA2's interaction with cFLIP (a decoy protein of the initiator procaspase-8 in the extrinsic apoptotic pathway) and deciphering the cFLIP's mode of cleavage, would provide an excellent alternative to modulate the pathway for therapeutic benefits toward diseases like ischemia and cancer.
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Affiliation(s)
- Kalyani Natu
- Integrated Biophysics and Structural Biology Lab, Advanced Centre for Treatment Research and Education in Cancer (ACTREC), Tata Memorial Centre, Mumbai, 410210, India
- Homi Bhabha National Institute, BARC Training School Complex, Mumbai, 400094, India
| | - Shubhankar Dutta
- Integrated Biophysics and Structural Biology Lab, Advanced Centre for Treatment Research and Education in Cancer (ACTREC), Tata Memorial Centre, Mumbai, 410210, India
- Homi Bhabha National Institute, BARC Training School Complex, Mumbai, 400094, India
| | - Kakoli Bose
- Integrated Biophysics and Structural Biology Lab, Advanced Centre for Treatment Research and Education in Cancer (ACTREC), Tata Memorial Centre, Mumbai, 410210, India
- Homi Bhabha National Institute, BARC Training School Complex, Mumbai, 400094, India
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23
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Abdjan MI, Shafiq M, Nerukh D, Nur-E-Alam M, Ul-Haq Z. Exploring the mechanism of action of spirooxindoles as a class of CDK2 inhibitors: a structure-based computational approach. Phys Chem Chem Phys 2024; 26:16139-16152. [PMID: 38787638 DOI: 10.1039/d4cp00844h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2024]
Abstract
Cyclin-dependent kinase 2 (CDK2) regulates cell cycle checkpoints in the synthesis and mitosis phases and plays a pivotal role in cancerous cell proliferation. The activation of CDK2, influenced by various protein signaling pathways, initiates the phosphorylation process. Due to its crucial role in carcinogenesis, CDK2 is a druggable hotspot target to suppress cancer cell proliferation. In this context, several studies have identified spirooxindoles as an effective class of CDK2 inhibitors. In the present study, three spirooxindoles (SOI1, SOI2, and SOI3) were studied to understand their inhibitory mechanism against CDK2 through a structure-based approach. Molecular docking and molecular dynamics (MD) simulations were performed to explore their interactions with CDK2 at the molecular level. The calculated binding free energy for the spirooxindole-based CDK2 inhibitors aligned well with experimental results regarding CDK2 inhibition. Energy decomposition (ED) analysis identified key binding residues, including I10, G11, T14, R36, F82, K89, L134, P155, T158, Y159, and T160, in the CDK2 active site and T-loop phosphorylation. Molecular mechanics (MM) energy was identified as the primary contributor to stabilizing inhibitor binding in the CDK2 protein structure. Furthermore, the analysis of binding affinity revealed that the inhibitor SOI1 binds more strongly to CDK2 compared to the other inhibitors under investigation. It demonstrated a robust interaction with the crucial residue T160 in the T-loop phosphorylation site, responsible for kinase activation. These insights into the inhibitory mechanism are anticipated to contribute to the development of potential CDK2 inhibitors using the spirooxindole scaffold.
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Affiliation(s)
- Muhammad Ikhlas Abdjan
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga, Komplek Kampus C UNAIR, Jl. Mulyorejo, Surabaya, Indonesia
| | - Muhammad Shafiq
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan
| | - Dmitry Nerukh
- Department of Mathematics, Aston University, Birmingham, B4 7ET, UK
| | - Mohammad Nur-E-Alam
- Department of Pharmacognosy, College of Pharmacy, King Saud University, P.O. Box. 2457, Riyadh 11451, Kingdom of Saudi Arabia.
| | - Zaheer Ul-Haq
- Dr Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan
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24
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Faris A, Hadni H, Saleh BA, Khelfaoui H, Harkati D, Ait Ahsaine H, Elhallaoui M, El-Hiti GA. In silico screening of a series of 1,6-disubstituted 1 H-pyrazolo[3,4- d]pyrimidines as potential selective inhibitors of the Janus kinase 3. J Biomol Struct Dyn 2024; 42:4456-4474. [PMID: 37317996 DOI: 10.1080/07391102.2023.2220829] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 05/28/2023] [Indexed: 06/16/2023]
Abstract
Rheumatoid arthritis is a common chronic disabling inflammatory disease that is characterized by inflammation of the synovial membrane and leads to discomfort. In the current study, twenty-seven 1,6-disubstituted 1H-pyrazolo[3,4-d]pyrimidines were tested as potential selective inhibitors of the tyrosine-protein kinase JAK3 using a number of molecular modeling methods. The activity of the screened derivatives was statistically quantified using multiple linear regression and artificial neural networks. To assess the quality, robustness, and predictability of the generated models, the leave-one-out cross-validation method was applied with favorable results (Q2 = 0.75) and Y-randomization. In addition, the evaluation of the predictive ability of the established model was confirmed by means of an external validation using a composite test set and an applicability domain approach. The covalent docking indicated that the tested 1H-pyrazolo[3,4-d]pyrimidines containing the acrylic aldehyde moiety had irreversible interaction with the residue Cys909 in the active sites of the tyrosine-protein kinase JAK3 by Michael addition. The molecular dynamics for three selected derivatives (compounds 9, 12, and 18) were used to verify the covalent docking by determining the stability of hydrogen bonding interactions with active sites, which are needed to stop tyrosine-protein kinase JAK3. The results obtained showed that the tested compounds containing acrylic aldehyde moiety had favorable binding free energies, indicating a strong affinity for the JAK3 enzyme. Overall, this current study suggests that the tested compounds containing the acrylic aldehyde moiety have the potential to act as anti-JAK3 inhibitors. They could be explored further to be used as treatment options for rheumatoid arthritis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Abdelmoujoud Faris
- LIMAS, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Hanine Hadni
- LIMAS, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Basil A Saleh
- Department of Chemistry, College of Science, University of Basrah, Basrah, Iraq
| | - Hadjer Khelfaoui
- Group of Computational and Pharmaceutical Chemistry, LMCE Laboratory, Faculty of Exact and Natural Sciences, Department of Matter Sciences, University of Biskra, Biskra, Algeria
| | - Dalal Harkati
- Group of Computational and Pharmaceutical Chemistry, LMCE Laboratory, Faculty of Exact and Natural Sciences, Department of Matter Sciences, University of Biskra, Biskra, Algeria
| | - Hassan Ait Ahsaine
- Laboratoire de Chimie Appliquée des Matériaux, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Menana Elhallaoui
- LIMAS, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Gamal A El-Hiti
- Department of Optometry, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
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25
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Choi J, Shin JY, Kim TK, Kim K, Kim J, Jeon E, Park J, Han YD, Kim KA, Sim T, Kim HK, Kim HS. Site-specific mutagenesis screening in KRAS G12D mutant library to uncover resistance mechanisms to KRAS G12D inhibitors. Cancer Lett 2024; 591:216904. [PMID: 38642608 DOI: 10.1016/j.canlet.2024.216904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 04/05/2024] [Accepted: 04/16/2024] [Indexed: 04/22/2024]
Abstract
KRAS plays a crucial role in regulating cell survival and proliferation and is one of the most commonly mutated oncogenes in human cancers. The novel KRASG12D inhibitor, MRTX1133, demonstrates promising antitumor efficacy in vitro and in vivo. However, the development of acquired resistance in treated patients presents a considerable challenge to sustained therapeutic effectiveness. In response to this challenge, we conducted site-specific mutagenesis screening to identify potential secondary mutations that could induce resistance to MRTX1133. We screened a range of KRASG12D variants harboring potential secondary mutations, and 44 representative variants were selected for in-depth validation of the pooled screening outcomes. We identified eight variants (G12D with V9E, V9W, V9Q, G13P, T58Y, R68G, Y96W, and Q99L) that exhibited substantial resistance, with V9W showing notable resistance, and downstream signaling analyses and structural modeling were conducted. We observed that secondary mutations in KRASG12D can lead to acquired resistance to MRTX1133 and BI-2865, a novel pan-KRAS inhibitor, in human cancer cell lines. This evidence is critical for devising new strategies to counteract resistance mechanisms and, ultimately, enhance treatment outcomes in patients with KRASG12D-mutant cancers.
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Affiliation(s)
- Jeesoo Choi
- Department of Internal Medicine, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Ju-Young Shin
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Taeyul K Kim
- Department of Internal Medicine, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Kiwook Kim
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Jiyun Kim
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Eunhye Jeon
- Severance Biomedical Science Institute, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Juyeong Park
- Department of Medicine, Graduate School, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea; Theragen Bio Co., Ltd, Seongnam-si, 13488, Republic of Korea
| | - Yoon Dae Han
- Department of Surgery, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Kyung-A Kim
- Department of Internal Medicine, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Taebo Sim
- Severance Biomedical Science Institute, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea; KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, 02841, Republic of Korea
| | - Hui Kwon Kim
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
| | - Han Sang Kim
- Department of Internal Medicine, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea; Yonsei Cancer Center, Division of Medical Oncology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.
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26
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Fülöp L. Carbohydrate polymer degradation derivatives as possible natural mannanase inhibitors. Int J Biol Macromol 2024; 269:132033. [PMID: 38702000 DOI: 10.1016/j.ijbiomac.2024.132033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 04/10/2024] [Accepted: 04/30/2024] [Indexed: 05/06/2024]
Abstract
The role of mannanases is diverse and they are used in many industrial applications, in animal feed, in the food industry and in healthcare. They are also applied in biomass processing, because they play an important role in the breakdown of hemicellulose. Among the mannanase inhibitors, heavy metal ions and general enzyme inhibitors are mainly mentioned. Unfortunately, almost no data are available on carbohydrate-based natural inhibitors of mannanases. According to the literature, carbohydrates do not play an important role in the inhibition of mannanases, so neither do oligosaccharides. This is in contrast to the action and inhibition of other O-glycosyl hydrolases. My hypothesis is that mannanases, like other polysaccharide-degrading enzymes, work in the same way and can be inhibited by oligosaccharides. Evidence from docking and modeling results supports and makes probable the hypothesis that oligosaccharides can inhibit the activity of mannanases, similar to the inhibition of other O-glycosyl hydrolases. Among natural carbohydrate oligomers, several potential mannanase inhibitors have been identified and characterized. In addition to expensive research, it is very important to use research based on cheaper modeling to explore the processes. The results obtained are novel and forward-looking, enabling in-depth and targeted research to be carried out.
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27
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Camacho RA, Machado AV, de Oliveira Mendonça F, Teixeira-Alves LR, Guimarães-Nobre CC, Mendonça-Reis E, da Silva PF, Cardim-Pires TR, Miranda-Alves L, Berto-Junior C. Unraveling DEHP influence on hemoglobin S polymerization in sickle cell disease: Ex vivo, in vitro and in silico analysis. Toxicol In Vitro 2024; 98:105832. [PMID: 38653437 DOI: 10.1016/j.tiv.2024.105832] [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: 10/03/2023] [Revised: 03/30/2024] [Accepted: 04/19/2024] [Indexed: 04/25/2024]
Abstract
Sickle cell disease (SCD) is a hereditary hemoglobinopathy, caused by a mutation at position 6 of the β-globin chain and patients are frequently exposed to several blood transfusions in order to maintain physiological function. Transfusion blood bags are composed of PVC and phthalates (as DEHP) are often introduced to the material in order to confer malleability. In this sense, DEHP can easily elute to the blood and cause harmful effects. This study aimed to unravel DEHP effect on SCD patient's hemoglobin function. We found that HbS polymerization using whole erythrocytes is decreased by DEHP in ex vivo experiments and this effect might be mediated by the DEHP-VAL6 interaction, evaluated in silico. Isolated HbS exhibited less polymerization at low DEHP concentrations and increased polymerization rate at higher concentration. When analyzing the propensity to aggregate, HbS is more inclined to aggregate when compared to HbA due to the residue 6 mutation. Circular dichroism showed characteristic hemoglobin peaks for oxygenated HbS that are lost when oxygen is sequestered, and DEHP at higher concentration mildly recovers a peak close to the second hemoglobin one. Finally, by transmission electron microscopy we demonstrated that high DEHP concentration increased polymer formation with a more organized structure. These findings show for the first-time the beneficial effect of low-dose DEHP on HbS polymerization.
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Affiliation(s)
- Rodrigo Abreu Camacho
- Grupo de Pesquisa em Fisiologia Eritróide - GPFisEri, Universidade Federal do Rio de Janeiro, Campus Macaé, Brazil; Programa de Pós-graduação em Endocrinologia, Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Brazil
| | - Aghata Vitoria Machado
- Grupo de Pesquisa em Fisiologia Eritróide - GPFisEri, Universidade Federal do Rio de Janeiro, Campus Macaé, Brazil; Instituto de Ciências Farmacêuticas, Universidade Federal do Rio de Janeiro, Centro Multidisciplinar UFRJ Macaé, Brazil
| | - Fernanda de Oliveira Mendonça
- Grupo de Pesquisa em Fisiologia Eritróide - GPFisEri, Universidade Federal do Rio de Janeiro, Campus Macaé, Brazil; Instituto de Ciências Farmacêuticas, Universidade Federal do Rio de Janeiro, Centro Multidisciplinar UFRJ Macaé, Brazil
| | - Lyzes Rosa Teixeira-Alves
- Grupo de Pesquisa em Fisiologia Eritróide - GPFisEri, Universidade Federal do Rio de Janeiro, Campus Macaé, Brazil; Programa de Pós-graduação em Endocrinologia, Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Brazil
| | - Camila Cristina Guimarães-Nobre
- Grupo de Pesquisa em Fisiologia Eritróide - GPFisEri, Universidade Federal do Rio de Janeiro, Campus Macaé, Brazil; Programa de Pós-graduação em Endocrinologia, Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Brazil; Instituto de Ciências Farmacêuticas, Universidade Federal do Rio de Janeiro, Centro Multidisciplinar UFRJ Macaé, Brazil
| | - Evelyn Mendonça-Reis
- Grupo de Pesquisa em Fisiologia Eritróide - GPFisEri, Universidade Federal do Rio de Janeiro, Campus Macaé, Brazil; Programa de Pós-graduação em Endocrinologia, Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Brazil
| | - Priscila Ferreira da Silva
- Universidade Federal do Rio de Janeiro, Centro Multidisciplinar UFRJ Macaé, Instituto de Ciências Farmacêuticas, Av. Aluizio da Silva Gomes, 50- Novo Cavaleiros, Macaé, 27930-560 Rio de Janeiro, RJ, Brazil
| | | | - Leandro Miranda-Alves
- Laboratório de Endocrinologia Experimental- LEEx, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Brazil; Programa de Pós-graduação em Endocrinologia, Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Brazil; Programa de Pós-graduação em Farmacologia e Química Medicinal, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Brazil
| | - Clemilson Berto-Junior
- Grupo de Pesquisa em Fisiologia Eritróide - GPFisEri, Universidade Federal do Rio de Janeiro, Campus Macaé, Brazil; Programa de Pós-graduação em Endocrinologia, Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Brazil; Instituto de Ciências Farmacêuticas, Universidade Federal do Rio de Janeiro, Centro Multidisciplinar UFRJ Macaé, Brazil.
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28
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Chompunud Na Ayudhya C, Graidist P, Tipmanee V. Role of CSF1R 550th-tryptophan in kusunokinin and CSF1R inhibitor binding and ligand-induced structural effect. Sci Rep 2024; 14:12531. [PMID: 38822100 PMCID: PMC11143223 DOI: 10.1038/s41598-024-63505-x] [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: 03/05/2024] [Accepted: 05/29/2024] [Indexed: 06/02/2024] Open
Abstract
Binding affinity is an important factor in drug design to improve drug-target selectivity and specificity. In this study, in silico techniques based on molecular docking followed by molecular dynamics (MD) simulations were utilized to identify the key residue(s) for CSF1R binding affinity among 14 pan-tyrosine kinase inhibitors and 15 CSF1R-specific inhibitors. We found tryptophan at position 550 (W550) on the CSF1R binding site interacted with the inhibitors' aromatic ring in a π-π way that made the ligands better at binding. Upon W550-Alanine substitution (W550A), the binding affinity of trans-(-)-kusunokinin and imatinib to CSF1R was significantly decreased. However, in terms of structural features, W550 did not significantly affect overall CSF1R structure, but provided destabilizing effect upon mutation. The W550A also did not either cause ligand to change its binding site or conformational changes due to ligand binding. As a result of our findings, the π-π interaction with W550's aromatic ring could be still the choice for increasing binding affinity to CSF1R. Nevertheless, our study showed that the increasing binding to W550 of the design ligand may not ensure CSF1R specificity and inhibition since W550-ligand bound state did not induce significantly conformational change into inactive state.
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Affiliation(s)
- Chompunud Chompunud Na Ayudhya
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Hat Yai, 90100, Songkhla, Thailand
| | - Potchanapond Graidist
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Hat Yai, 90100, Songkhla, Thailand
- Bioactivity Testing Center, Faculty of Medicine, Prince of Songkla University, Hat Yai, 90100, Songkhla, Thailand
| | - Varomyalin Tipmanee
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Hat Yai, 90100, Songkhla, Thailand.
- Bioactivity Testing Center, Faculty of Medicine, Prince of Songkla University, Hat Yai, 90100, Songkhla, Thailand.
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29
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Revanasiddappa PD, H. G. G, K. P. C, Natarajamurthy S, K. N, Pradeep S, Shivamallu C, Elossaily GM, Achar RR, Silina E, Stupin V, Manturova N, A. Shati A, Y. Alfaifi M, I. Elbehairi SE, Kestur Nagaraj A, Mahadevamurthy M, Kollur SP. Computational exploration of Picrasma quassioides compounds as CviR-mediated quorum sensing inhibitors against Chromobacterium violaceum. Front Chem 2024; 12:1286675. [PMID: 38867763 PMCID: PMC11167448 DOI: 10.3389/fchem.2024.1286675] [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: 09/06/2023] [Accepted: 04/17/2024] [Indexed: 06/14/2024] Open
Abstract
Chromobacterium violaceum an opportunistic human pathogenic bacterium, exhibits resistance to conventional antibiotics by exploiting its quorum sensing mechanism to regulate virulence factor expression. In light of this, disrupting the quorum sensing mechanism presents a promising avenue for treating infections caused by this pathogen. The study focused on using the cytoplasmic quorum sensing receptor CviR from C. violaceum as a model target to identify novel quorum sensing inhibitors from P. quassioides through in silico computational approaches. Molecular docking analyses unveiled that several phytochemicals derived from Picrasma quassioides exhibit the potential to inhibit quorum sensing by binding to CviR protein. Notably, the compounds such as Quassidine I (- 8.8 kcal/mol), Quassidine J (- 8.8 kcal/mol), Kumudine B (- 9.1 kcal/mol) and Picrasamide A (- 8.9 kcal/mol) exhibited high docking scores, indicating strong binding affinity to the CviR protein. The native ligand C6-HSL (N-hexanoyl-L-homoserine lactone) as a positive control/co-crystal inhibitor also demonstrated a significant binding energy of-7.7 kcal/mol. The molecular dynamics simulation for 200 ns showed the thermodynamic stability and binding affinity refinement of the top-ranked CviR inhibitor (Kumudine B) with its stable binding and minor fluctuations compared to positive control (C6-HSL). Pharmacokinetic predictions indicated that Kumudine B possesses favourable drug-like properties, which suggest its potential as a drug candidate. The study highlight Kumudine B as a potential agent for inhibiting the CviR protein in C. violaceum. The comprehensive evaluation of Kumudine B provides valuable insights into its pharmacological profiles, facilitating its assessment for diverse therapeutic applications and guiding future research activities, particularly as antibacterial agents for clinical drug development.
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Affiliation(s)
| | - Gowtham H. G.
- Department of Studies and Research in Food Science and Nutrition, Karnataka State Open University, Mysuru, India
| | - Chandana K. P.
- Department of Biotechnology, Siddaganga Institute of Technology, Tumkur, India
| | | | - Nataraj K.
- Department of Studies in Botany, University of Mysore, Mysore, India
| | - Sushma Pradeep
- Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru, India
| | - Chandan Shivamallu
- Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru, India
| | - Gehan M. Elossaily
- Department of Basic Medical Sciences, College of Medicine, AlMaarefa University, Riyadh, Saudi Arabia
| | - Raghu Ram Achar
- Division of Biochemistry, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru, India
| | - Ekaterina Silina
- Department of Pathophysiology, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Victor Stupin
- Department of Hospital Surgery, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Natalia Manturova
- Department of Hospital Surgery, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Ali A. Shati
- Biology Department, Faculty of Science, King Khalid University, Abha, Saudi Arabia
| | - Mohammad Y. Alfaifi
- Biology Department, Faculty of Science, King Khalid University, Abha, Saudi Arabia
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Babijczuk K, Berdzik N, Nowak D, Warżajtis B, Rychlewska U, Starzyk J, Mrówczyńska L, Jasiewicz B. Novel C3-Methylene-Bridged Indole Derivatives with and without Substituents at N1: The Influence of Substituents on Their Hemolytic, Cytoprotective, and Antimicrobial Activity. Int J Mol Sci 2024; 25:5364. [PMID: 38791402 PMCID: PMC11121452 DOI: 10.3390/ijms25105364] [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: 04/15/2024] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
Alkaloids are natural compounds useful as scaffolds for discovering new bioactive molecules. This study utilized alkaloid gramine to synthesize two groups of C3-substituted indole derivatives, which were either functionalized at N1 or not. The compounds were characterized by spectroscopic methods. The protective effects of the new compounds against in vitro oxidative hemolysis induced by standard oxidant 2,2'-azobis(2-amidinopropane dihydro chloride (AAPH) on human erythrocytes as a cell model were investigated. Additionally, the compounds were screened for antimicrobial activity. The results indicated that most of the indole derivatives devoid of the N1 substitution exhibited strong cytoprotective properties. The docking studies supported the affinities of selected indole-based ligands as potential antioxidants. Furthermore, the derivatives obtained exhibited potent fungicidal properties. The structures of the eight derivatives possessing indole moiety bridged to the imidazole-, benzimidazole-, thiazole-, benzothiazole-, and 5-methylbenzothiazoline-2-thiones were determined by X-ray diffraction. The C=S bond lengths in the thioamide fragment pointed to the involvement of zwitterionic structures of varying contribution. The predominance of zwitterionic mesomers may explain the lack of cytoprotective properties, while steric effects, which limit multiple the hydrogen-bond acceptor properties of a thione sulfur, seem to be responsible for the high hemolytic activity.
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Affiliation(s)
- Karolina Babijczuk
- Department of Bioactive Products, Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614 Poznań, Poland; (K.B.); (N.B.)
| | - Natalia Berdzik
- Department of Bioactive Products, Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614 Poznań, Poland; (K.B.); (N.B.)
| | - Damian Nowak
- Department of Quantum Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614 Poznań, Poland;
| | - Beata Warżajtis
- Department of Crystallography, Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614 Poznań, Poland; (B.W.); (U.R.)
| | - Urszula Rychlewska
- Department of Crystallography, Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614 Poznań, Poland; (B.W.); (U.R.)
| | - Justyna Starzyk
- Department of Soil Science and Microbiology, Faculty of Agronomy, Horticulture, and Bioengineering, University of Life Science, Szydłowska 50, 60-656 Poznań, Poland;
| | - Lucyna Mrówczyńska
- Department of Cell Biology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland;
| | - Beata Jasiewicz
- Department of Bioactive Products, Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614 Poznań, Poland; (K.B.); (N.B.)
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Hawash M, Abdallah S, Abudayyak M, Melhem Y, Abu Shamat M, Aghbar M, Çapan I, Abualhasan M, Kumar A, Kamiński M, Góral T, Dominiak PM, Sobuh S. Exploration of isoxazole analogs: Synthesis, COX inhibition, anticancer screening, 3D multicellular tumor spheroids, and molecular modeling. Eur J Med Chem 2024; 271:116397. [PMID: 38626522 DOI: 10.1016/j.ejmech.2024.116397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 04/05/2024] [Accepted: 04/06/2024] [Indexed: 04/18/2024]
Abstract
In this study, a new series of Isoxazole-carboxamide derivatives were synthesized and characterized via HRMS, 1H-, 13CAPT-NMR, and MicroED. The findings revealed that nearly all of the synthesized derivatives exhibited potent inhibitory activities against both COX enzymes, with IC50 values ranging from 4.1 nM to 3.87 μM. Specifically, MYM1 demonstrated the highest efficacy among the compounds tested against the COX-1, displaying an IC50 value of 4.1 nM. The results showed that 5 compounds possess high COX-2 isozyme inhibitory effects with IC50 value in range 0.24-1.30 μM with COX-2 selectivity indexes (2.51-6.13), among these compounds MYM4 has the lowest IC50 value against COX-2, with selectivity index around 4. Intriguingly, this compound displayed significant antiproliferative effects against CaCo-2, Hep3B, and HeLa cancer cell lines, with IC50 values of 10.22, 4.84, and 1.57 μM, respectively, which was nearly comparable to that of doxorubicin. Compound MYM4 showed low cytotoxic activities on normal cell lines LX-2 and Hek293t with IC50 values 20.01 and 216.97 μM respectively, with safer values than doxorubicin. Furthermore, compound MYM4 was able to induce the apoptosis, suppress the colonization of both HeLa and HepG2 cells. Additionally, the induction of Reactive oxygen species (ROS) production could be the mechanism underlying the apoptotic effect and the cytotoxic activity of the compound. In the 3D multicellular tumor spheroid model, results revealed that MYM4 compound hampered the spheroid formation capacity of Hep3B and HeLa cancer cells. Moreover, the molecular docking of MYM4 compound revealed a high affinity for the COX2 enzyme, with energy scores (S) -7.45 kcal/mol, which were comparable to celecoxib (S) -8.40 kcal/mol. Collectively, these findings position MYM4 as a promising pharmacological candidate as COX inhibitor and anticancer agent.
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Affiliation(s)
- Mohammed Hawash
- Department of Pharmacy, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus, 00970, Palestine.
| | - Samer Abdallah
- Department of Biology & Biotechnology, Faculty of Science, An-Najah National University, Nablus, 00970, Palestine
| | - Mahmoud Abudayyak
- Faculty of Pharmacy, Department of Pharmaceutical Toxicology, Istanbul University, 34116, Istanbul, Turkey
| | - Yarob Melhem
- Department of Pharmacy, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus, 00970, Palestine
| | - Mohammed Abu Shamat
- Department of Pharmacy, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus, 00970, Palestine
| | - Meera Aghbar
- Department of Pharmacy, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus, 00970, Palestine
| | - Irfan Çapan
- Department of Material and Material Processing Technologies, Technical Sciences Vocational College, Gazi University, 06560, Ankara, Turkey; Basic and Engineering Sciences Central Laboratory Application and Research Center (GUTMAM), Gazi University, 06500, Ankara, Turkey
| | - Murad Abualhasan
- Department of Pharmacy, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus, 00970, Palestine
| | - Anil Kumar
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Ul. Zwirki I Wigury 101, 02-089, Warsaw, Poland
| | - Michał Kamiński
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Ul. Zwirki I Wigury 101, 02-089, Warsaw, Poland
| | - Tomasz Góral
- Centre of New Technologies, University of Warsaw, Ul. S. Banacha 2c, 02-097, Warsaw, Poland
| | - Paulina Maria Dominiak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Ul. Zwirki I Wigury 101, 02-089, Warsaw, Poland
| | - Shorooq Sobuh
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus, 00970, Palestine
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Rasul HO, Thomas NV, Ghafour DD, Aziz BK, Salgado M G, Mendoza-Huizar LH, Candia LG. Searching possible SARS-CoV-2 main protease inhibitors in constituents from herbal medicines using in silico studies. J Biomol Struct Dyn 2024; 42:4234-4248. [PMID: 37349945 DOI: 10.1080/07391102.2023.2220040] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 05/23/2023] [Indexed: 06/24/2023]
Abstract
The largest threat to civilization since the Second World War is the spread of the new coronavirus disease (COVID-19). Therefore, there is an urgent need for innovative therapeutic medicines to treat COVID-19. Reusing bio-actives is a workable and efficient strategy in the battle against new epidemics because the process of developing new drugs is time-consuming. This research aimed to identify which herbal remedies had the highest affinity for the receptor and assess a variety of them for potential targets to suppress the SARS-CoV-2 Mpro. The use of AutoDock Vina for structure-based virtual screening was done first due to the importance of protein interactions in the development of drugs. Molecular docking was used in the comparative study to assess 89 different chemicals from medicinal herbs. To anticipate their effectiveness against the primary protease of SARS-CoV-2, more analysis was done on the ADMET profile, drug-likeness, and Lipinski's rule of five. The next step involved three replicas of 100 ns-long molecular dynamics simulations on the potential candidates, which were preceded by calculations of the binding free energy of MM-GBSA. The outcomes showed that Achyrodimer A, Cinchonain Ib, Symphonone F, and Lupeol acetate all performed well and had the highest 6LU7 binding affinities. Using RMSD, RMSF, and protein-ligand interactions, the stability of the protein-ligand complex was assessed. The studies indicate that bioactive substances obtained from herbal medicines may function as a COVID-19 therapeutic agent, necessitating additional wet lab research to confirm their therapeutic potential, efficacy, and pharmacological capacity against the condition.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hezha O Rasul
- Department of Pharmaceutical Chemistry, College of Science, Charmo University, Chamchamal, Sulaimani, Iraq
| | - Noel Vinay Thomas
- Department of BioMedical Science, College of Science, Komar University of Science and Technology, Sulaimani, Iraq
| | - Dlzar D Ghafour
- Department of Medical Laboratory Science, College of Science, Komar University of Science and Technology, Sulaimani, Iraq
- Department of Chemistry, College of Science, University of Sulaimani, Sulaimani, Iraq
| | - Bakhtyar K Aziz
- Department of Nanoscience and Applied Chemistry, College of Science, Charmo University, Chamchamal, Sulaimani, Iraq
| | | | - L H Mendoza-Huizar
- Academic Area of Chemistry, Mineral de la Reforma, Autonomous University of Hidalgo State, Hidalgo, México
| | - Lorena Gerli Candia
- Departamento de Química Ambiental, Facultad de Ciencias, Universidad Católica de la Santísima Concepción, Concepción, Chile
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Mslati H, Gentile F, Pandey M, Ban F, Cherkasov A. PROTACable Is an Integrative Computational Pipeline of 3-D Modeling and Deep Learning To Automate the De Novo Design of PROTACs. J Chem Inf Model 2024; 64:3034-3046. [PMID: 38504115 DOI: 10.1021/acs.jcim.3c01878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Proteolysis-targeting chimeras (PROTACs) that engage two biological targets at once are a promising technology in degrading clinically relevant protein targets. Since factors that influence the biological activities of PROTACs are more complex than those of a small molecule drug, we explored a combination of computational chemistry and deep learning strategies to forecast PROTAC activity and enable automated design. A new method named PROTACable was developed for the de novo design of PROTACs, which includes a robust 3-D modeling workflow to model PROTAC ternary complexes using a library of E3 ligase and linker and an SE(3)-equivariant graph transformer network to predict the activity of newly designed PROTACs. PROTACable is available at https://github.com/giaguaro/PROTACable/.
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Affiliation(s)
- Hazem Mslati
- Vancouver Prostate Centre, The University of British Columbia, Vancouver, British Columbia V6H 3Z6, Canada
| | - Francesco Gentile
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
- Ottawa Institute of Systems Biology, Ottawa, Ontario K1N 6N5, Canada
| | - Mohit Pandey
- Vancouver Prostate Centre, The University of British Columbia, Vancouver, British Columbia V6H 3Z6, Canada
| | - Fuqiang Ban
- Vancouver Prostate Centre, The University of British Columbia, Vancouver, British Columbia V6H 3Z6, Canada
| | - Artem Cherkasov
- Vancouver Prostate Centre, The University of British Columbia, Vancouver, British Columbia V6H 3Z6, Canada
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Samykannu G, Mariyappan N, Natarajan J. Molecular interaction and MD-simulations: investigation of Sizofiran as a promising anti-cancer agent targeting eIF4E in colorectal cancer. In Silico Pharmacol 2024; 12:33. [PMID: 38655099 PMCID: PMC11033251 DOI: 10.1007/s40203-024-00206-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 03/28/2024] [Indexed: 04/26/2024] Open
Abstract
CRC has a major global health impact due to high mortality rates. CRC shows high expression of eukaryotic translation initiation factor (eIF4E) protein, the rapid development of lung, bladder, colon, prostate, breast, head, and neck cancer is attributed to the dysregulation of eIF4E making an important target for treatment. Targeting eIF4E-mediated translation is a promising anti-cancer strategy. Many organic compounds that inhibit eIF4E are being studied clinically. The compound Sizofiran has emerged as a promising eIF4E inhibitor candidate, but its exact mechanism of action is unclear. In an effort to close this discrepancy by clarifying the mechanism of the interactions between phytochemical substances and eIF4E, molecular docking and dynamics studies were conducted. Molecular docking studies found Sizofiran (- 12.513 kcal/mol) has the most affinity eIF4E binding energy out of 93 phytochemicals, 5 current drugs, and 4 known inhibitors. This positions it as a top eIF4E inhibitor candidate. An alignment of eIF4E protein sequences from multiple pathogens revealed that the glutamate103 interacting residues are evolutionarily conserved across the different eIF4E proteins. Further insights from 100 ns of MD simulations supported Sizofiran having superior stability and eIF4E inhibition compared to reference compounds. Designed Sizofiran-related compounds showed better activity than the current drugs such as Camptosar, Sorafenib, Regorafenib, Doxorubicin, and Kenpaullone, indicating strong potential to suppress CRC progression by targeting eIF4E. This research aims to significantly aid development of improved eIF4E-targeting drugs for cancer treatment. Graphical abstract Showing the Graphical abstract of the complete study. Supplementary Information The online version contains supplementary material available at 10.1007/s40203-024-00206-3.
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Affiliation(s)
- Gopinath Samykannu
- Data Mining and Text Mining Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore, TamilNadu India
| | - Nandhini Mariyappan
- Molecular Modelling and Designing Laboratory, Department of Physics, Bharathiar University, Coimbatore, TamilNadu India
| | - Jeyakumar Natarajan
- Data Mining and Text Mining Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore, TamilNadu India
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Pang C, Qiao J, Zeng X, Zou Q, Wei L. Deep Generative Models in De Novo Drug Molecule Generation. J Chem Inf Model 2024; 64:2174-2194. [PMID: 37934070 DOI: 10.1021/acs.jcim.3c01496] [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] [Indexed: 11/08/2023]
Abstract
The discovery of new drugs has important implications for human health. Traditional methods for drug discovery rely on experiments to optimize the structure of lead molecules, which are time-consuming and high-cost. Recently, artificial intelligence has exhibited promising and efficient performance for drug-like molecule generation. In particular, deep generative models achieve great success in de novo generation of drug-like molecules with desired properties, showing massive potential for novel drug discovery. In this study, we review the recent progress of molecule generation using deep generative models, mainly focusing on molecule representations, public databases, data processing tools, and advanced artificial intelligence based molecule generation frameworks. In particular, we present a comprehensive comparison of state-of-the-art deep generative models for molecule generation and a summary of commonly used molecular design strategies. We identify research gaps and challenges of molecule generation such as the need for better databases, missing 3D information in molecular representation, and the lack of high-precision evaluation metrics. We suggest future directions for molecular generation and drug discovery.
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Affiliation(s)
- Chao Pang
- School of Software, Shandong University, Jinan 250100, China
- Joint SDU-NTU Centre for Artificial Intelligence Research (C-FAIR), Shandong University, Jinan 250100, China
| | - Jianbo Qiao
- School of Software, Shandong University, Jinan 250100, China
- Joint SDU-NTU Centre for Artificial Intelligence Research (C-FAIR), Shandong University, Jinan 250100, China
| | - Xiangxiang Zeng
- College of Information Science and Engineering, Hunan University, Changsha 410082, China
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Leyi Wei
- School of Software, Shandong University, Jinan 250100, China
- Joint SDU-NTU Centre for Artificial Intelligence Research (C-FAIR), Shandong University, Jinan 250100, China
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Nkungli NK, Fouegue ADT, Tasheh SN, Bine FK, Hassan AU, Ghogomu JN. In silico investigation of falcipain-2 inhibition by hybrid benzimidazole-thiosemicarbazone antiplasmodial agents: A molecular docking, molecular dynamics simulation, and kinetics study. Mol Divers 2024; 28:475-496. [PMID: 36622482 PMCID: PMC9838286 DOI: 10.1007/s11030-022-10594-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 12/20/2022] [Indexed: 01/10/2023]
Abstract
The emergence of artemisinin-resistant variants of Plasmodium falciparum necessitates the urgent search for novel antimalarial drugs. In this regard, an in silico study to screen antimalarial drug candidates from a series of benzimidazole-thiosemicarbazone hybrid molecules with interesting antiplasmodial properties and explore their falcipain-2 (FP2) inhibitory potentials has been undertaken herein. FP2 is a key cysteine protease that degrades hemoglobin in Plasmodium falciparum and is an important biomolecular target in the development of antimalarial drugs. Pharmacokinetic properties, ADMET profiles, MM/GBSA-based binding free energies, reaction mechanisms, and associated barrier heights have been investigated. DFT, molecular dynamics simulation, molecular docking, and ONIOM methods were used. From the results obtained, four 4N-substituted derivatives of the hybrid molecule (E)-2-(1-(5-chloro-1H-benzo[d]imidazol-2-yl)ethylidene)hydrazine-1-carbothioamide (1A) denoted 1B, 1C, 1D, and 1E are drug-like and promising inhibitors of FP2, exhibiting remarkably small inhibitory constants (5.94 × 10-14 - 2.59 × 10-04 n M) and favorable binding free energies (-30.32 to -17.17 kcal/mol). Moreover, the ONIOM results have revealed that 1B and possibly 1C and 1D may act as covalent inhibitors of FP2. The rate-determining step of the thermodynamically favorable covalent binding mechanism occurs across a surmountable barrier height of 24.18 kcal/mol in water and 28.42 kcal/mol in diethyl ether. Our findings are useful for further experimental investigations on the antimalarial activities of the hybrid molecules studied.
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Affiliation(s)
- Nyiang Kennet Nkungli
- Department of Chemistry, Faculty of Science, The University of Bamenda, Bambili, P. O. Box 39, Bamenda, Cameroon.
| | - Aymard Didier Tamafo Fouegue
- Department of Chemistry, Higher Teacher Training College Bertoua, University of Bertoua, P.O. Box 652, Bertoua, Cameroon
| | - Stanley Numbonui Tasheh
- Department of Chemistry, Faculty of Science, The University of Bamenda, Bambili, P. O. Box 39, Bamenda, Cameroon
- Department of Chemistry, Faculty of Science, University of Dschang, P. O. Box 67, Dschang, Cameroon
| | - Fritzgerald Kogge Bine
- Department of Chemistry, Faculty of Science, University of Dschang, P. O. Box 67, Dschang, Cameroon
| | - Abrar Ul Hassan
- Department of Chemistry, University of Gujrat, Gujrat, 54400, PK, Pakistan
| | - Julius Numbonui Ghogomu
- Department of Chemistry, Faculty of Science, The University of Bamenda, Bambili, P. O. Box 39, Bamenda, Cameroon
- Department of Chemistry, Faculty of Science, University of Dschang, P. O. Box 67, Dschang, Cameroon
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Wang Z, Wang S, Li Y, Guo J, Wei Y, Mu Y, Zheng L, Li W. A new paradigm for applying deep learning to protein-ligand interaction prediction. Brief Bioinform 2024; 25:bbae145. [PMID: 38581420 PMCID: PMC10998640 DOI: 10.1093/bib/bbae145] [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: 11/06/2023] [Revised: 02/21/2024] [Accepted: 03/18/2024] [Indexed: 04/08/2024] Open
Abstract
Protein-ligand interaction prediction presents a significant challenge in drug design. Numerous machine learning and deep learning (DL) models have been developed to accurately identify docking poses of ligands and active compounds against specific targets. However, current models often suffer from inadequate accuracy or lack practical physical significance in their scoring systems. In this research paper, we introduce IGModel, a novel approach that utilizes the geometric information of protein-ligand complexes as input for predicting the root mean square deviation of docking poses and the binding strength (pKd, the negative value of the logarithm of binding affinity) within the same prediction framework. This ensures that the output scores carry intuitive meaning. We extensively evaluate the performance of IGModel on various docking power test sets, including the CASF-2016 benchmark, PDBbind-CrossDocked-Core and DISCO set, consistently achieving state-of-the-art accuracies. Furthermore, we assess IGModel's generalizability and robustness by evaluating it on unbiased test sets and sets containing target structures generated by AlphaFold2. The exceptional performance of IGModel on these sets demonstrates its efficacy. Additionally, we visualize the latent space of protein-ligand interactions encoded by IGModel and conduct interpretability analysis, providing valuable insights. This study presents a novel framework for DL-based prediction of protein-ligand interactions, contributing to the advancement of this field. The IGModel is available at GitHub repository https://github.com/zchwang/IGModel.
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Affiliation(s)
- Zechen Wang
- School of Physics, Shandong University, South Shanda Road, 250100 Shandong, China
| | - Sheng Wang
- Shanghai Zelixir Biotech, Xiangke Road, 200030, Shanghai, China
| | - Yangyang Li
- School of Physics, Shandong University, South Shanda Road, 250100 Shandong, China
| | - Jingjing Guo
- Centre in Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Rua de Luís Gonzaga Gomes, Macao, China
| | - Yanjie Wei
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Xueyuan Road 1068, Shenzhen, 518055 Guang Dong, China
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Liangzhen Zheng
- Shanghai Zelixir Biotech, Xiangke Road, 200030, Shanghai, China
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Xueyuan Road 1068, Shenzhen, 518055 Guang Dong, China
| | - Weifeng Li
- School of Physics, Shandong University, South Shanda Road, 250100 Shandong, China
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38
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Salih OM, Al-Sha’er MA, Basheer HA. Novel 2-Aminobenzothiazole Derivatives: Docking, Synthesis, and Biological Evaluation as Anticancer Agents. ACS OMEGA 2024; 9:13928-13950. [PMID: 38559989 PMCID: PMC10975593 DOI: 10.1021/acsomega.3c09212] [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: 11/18/2023] [Revised: 02/09/2024] [Accepted: 02/28/2024] [Indexed: 04/04/2024]
Abstract
Sixteen novel 2-aminobenzothiazole compounds with different amines or substituted piperazine moieties were designed, synthesized, and tested using various methods. Potential interactions were assessed by docking new compounds in the adenosine triphosphate (ATP) binding domain of the PI3Kγ enzyme (PDB code: 7JWE) by nucleophilic substitution or solvent-free/neat fusion for docked compound synthesis. Final 2-aminobenzothiazole compounds were characterized by direct probe gas chromatography-mass spectrometry (GC-MS), proton (1H-NMR), carbon-13 (13C-NMR), and attenuated total reflectance-infrared Fourier transform infrared (ATR FT-IR). The synthesized compounds were investigated for anticancer activities on lung cancer (A549) and breast cancer (MCF-7) cell lines. The compounds' PI3Kγ inhibition was evaluated at a 100 μM concentration. 4-Nitroaniline and piperazine-4-nitroaniline combination in OMS5 and OMS14 reduced lung and breast cancer cell line growth. IC50 values for OMS5 and OMS14, the strongest compounds, ranged from 22.13 to 61.03 μM. OMS1 and OMS2 inhibited PI3Kγ at the highest rates (47 and 48%, respectively) at a 100 μM concentration. Results show that the PI3Kγ enzyme suppression is not the main mechanism behind these OMS5 and OMS14 anticancer effects. CDK2, Akt, mTOR, and p42/44 MAPK are affected. EGF receptor suppression matters. AKT1, AKT3, CDK1/cyclin B, PDK1 direct, PIK3CA E542 K/PIK3R1 (p110 α/p85 α), PIK3CD/PIK3R1 (p110 δ/p85 α), and PKN inhibition were measured to evaluate the possible mechanism of compound OMS14. PIK3CD/PIK3R1 (p110 δ/p85 α) is the most, with 65% inhibition, suggesting a possible mechanism of anticancer properties. Furthermore, the NCI 60-cell line inhibition demonstrates promising broad anticancer inhibition against numerous cancer cell lines of OMS5 and OMS14, which could be good lead compounds for future development.
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Affiliation(s)
- Omar M. Salih
- Pharmaceutical
Sciences Department, College of Pharmacy, Zarqa University, Zarqa 13132, Jordan
| | - Mahmoud A. Al-Sha’er
- Pharmaceutical
Sciences Department, College of Pharmacy, Zarqa University, Zarqa 13132, Jordan
| | - Haneen A. Basheer
- Clinical
Pharmacy Department, College of Pharmacy, Zarqa University, Zarqa 13132, Jordan
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El-Sayed GM, Emam MTH, Hammad MA, Mahmoud SH. Gene Cloning, Heterologous Expression, and In Silico Analysis of Chitinase B from Serratia marcescens for Biocontrol of Spodoptera frugiperda Larvae Infesting Maize Crops. Molecules 2024; 29:1466. [PMID: 38611746 PMCID: PMC11012731 DOI: 10.3390/molecules29071466] [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: 02/18/2024] [Revised: 03/14/2024] [Accepted: 03/18/2024] [Indexed: 04/14/2024] Open
Abstract
Spodoptera frugiperda, the fall armyworm (FAW), is a highly invasive polyphagous insect pest that is considered a source of severe economic losses to agricultural production. Currently, the majority of chemical insecticides pose tremendous threats to humans and animals besides insect resistance. Thus, there is an urgent need to develop new pest management strategies with more specificity, efficiency, and sustainability. Chitin-degrading enzymes, including chitinases, are promising agents which may contribute to FAW control. Chitinase-producing microorganisms are reported normally in bacteria and fungi. In the present study, Serratia marcescens was successfully isolated and identified from the larvae of Spodoptera frugiperda. The bacterial strain NRC408 displayed the highest chitinase enzyme activity of 250 units per milligram of protein. Subsequently, the chitinase gene was cloned and heterologously expressed in E. coli BL21 (DE3). Recombinant chitinase B was overproduced to 2.5-fold, driven by the T7 expression system. Recombinant chitinase B was evaluated for its efficacy as an insecticidal bioagent against S. frugiperda larvae, which induced significant alteration in subsequent developmental stages and conspicuous malformations. Additionally, our study highlights that in silico analyses of the anticipated protein encoded by the chitinase gene (ChiB) offered improved predictions for enzyme binding and catalytic activity. The effectiveness of (ChiB) against S. frugiperda was evaluated in laboratory and controlled field conditions. The results indicated significant mortality, disturbed development, different induced malformations, and a reduction in larval populations. Thus, the current study consequently recommends chitinase B for the first time to control FAW.
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Affiliation(s)
- Ghada M. El-Sayed
- Microbial Genetic Department, Biotechnology Research Institute, National Research Centre, 33 El-Bohouth St. (Former El-Tahrir St.), Dokki, Cairo 12622, Egypt
| | - Maha T. H. Emam
- Genetics & Cytology Department, Biotechnology Research Institute, National Research Centre, 33 El-Bohouth St. (Former El-Tahrir St.), Dokki, Cairo 12622, Egypt;
| | - Maher A. Hammad
- Department of Plant Protection, Faculty of Agriculture, Ain Shams University, Cairo 11566, Egypt
| | - Shaymaa H. Mahmoud
- Zoology Department, Faculty of Science, Menoufia University, Shibin El Kom 32511, Egypt;
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Ramli AH, Swain P, Mohd Fahmi MSA, Abas F, Leong SW, Tejo BA, Shaari K, Ali AH, Agustar HK, Awang R, Ng YL, Lau YL, Md Razali MA, Mastuki SN, Mohmad Misnan N, Mohd Faudzi SM, Kim CH. Preliminary insight on diarylpentanoids as potential antimalarials: In silico, in vitro pLDH and in vivo zebrafish toxicity assessment. Heliyon 2024; 10:e27462. [PMID: 38495201 PMCID: PMC10943399 DOI: 10.1016/j.heliyon.2024.e27462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 02/28/2024] [Accepted: 02/29/2024] [Indexed: 03/19/2024] Open
Abstract
Malaria remains a major public health problem worldwide, including in Southeast Asia. Chemotherapeutic agents such as chloroquine (CQ) are effective, but problems with drug resistance and toxicity have necessitated a continuous search for new effective antimalarial agents. Here we report on a virtual screening of ∼300 diarylpentanoids and derivatives, in search of potential Plasmodium falciparum lactate dehydrogenase (PfLDH) inhibitors with acceptable drug-like properties. Several molecules with binding affinities comparable to CQ were chosen for in vitro validation of antimalarial efficacy. Among them, MS33A, MS33C and MS34C are the most promising against CQ-sensitive (3D7) with EC50 values of 1.6, 2.5 and 3.1 μM, respectively. Meanwhile, MS87 (EC50 of 1.85 μM) shown the most active against the CQ-resistant Gombak A strain, and MS33A and MS33C the most effective P. knowlesi inhibitors (EC50 of 3.6 and 5.1 μM, respectively). The in vitro cytotoxicity of selected diarylpentanoids (MS33A, MS33C, MS34C and MS87) was tested on Vero mammalian cells to evaluate parasite selectivity (SI), showing moderate to low cytotoxicity (CC50 > 82 μM). In addition, MS87 exhibited a high SI and the lowest resistance index (RI), suggesting that MS87 may exert effective parasite inhibition with low resistance potential in the CQ-resistant P. falciparum strain. Furthermore, the in vivo toxicity of the molecules on early embryonic development, the cardiovascular system, heart rate, motor activity and apoptosis were assessed in a zebrafish animal model. The overall results indicate the preliminary potential of diarylpentanoids, which need further investigation for their development as new antimalarial agents.
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Affiliation(s)
- Amirah Hani Ramli
- Natural Medicines and Product Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, Serdang, 43400, Selangor, Malaysia
| | - Puspanjali Swain
- Department of Biology, Chungnam National University, Daejeon, 34134, South Korea
| | - Muhammad Syafiq Akmal Mohd Fahmi
- Natural Medicines and Product Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, Serdang, 43400, Selangor, Malaysia
| | - Faridah Abas
- Natural Medicines and Product Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, Serdang, 43400, Selangor, Malaysia
- Department of Food Science, Faculty of Food Science & Technology, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Sze Wei Leong
- Department of Chemistry, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Bimo Ario Tejo
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Khozirah Shaari
- Natural Medicines and Product Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, Serdang, 43400, Selangor, Malaysia
| | - Amatul Hamizah Ali
- Department of Earth Sciences and Environment, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, 43600, Selangor, Malaysia
| | - Hani Kartini Agustar
- Department of Earth Sciences and Environment, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, 43600, Selangor, Malaysia
| | - Rusdam Awang
- UPM - MAKNA Cancer Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Yee Ling Ng
- Department of Parasitology, Faculty of Medicine, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Yee Ling Lau
- Department of Parasitology, Faculty of Medicine, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | | | - Siti Nurulhuda Mastuki
- Natural Medicines and Product Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, Serdang, 43400, Selangor, Malaysia
- Department of Biological Sciences and Biotechnology, Faculty of Science & Technology, Universiti Kebangsaan Malaysia, Bangi, 43600, Selangor, Malaysia
| | - Norazlan Mohmad Misnan
- Herbal Medicine Research Centre, Institute for Medical Research, National Institutes of Health, 40170, Shah Alam, Selangor Darul Ehsan, Malaysia
| | - Siti Munirah Mohd Faudzi
- Natural Medicines and Product Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, Serdang, 43400, Selangor, Malaysia
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Cheol-Hee Kim
- Department of Biology, Chungnam National University, Daejeon, 34134, South Korea
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Ashley CN, Broni E, Wood CM, Okuneye T, Ojukwu MPT, Dong Q, Gallagher C, Miller WA. Identifying potential monkeypox virus inhibitors: an in silico study targeting the A42R protein. Front Cell Infect Microbiol 2024; 14:1351737. [PMID: 38500508 PMCID: PMC10945028 DOI: 10.3389/fcimb.2024.1351737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 02/19/2024] [Indexed: 03/20/2024] Open
Abstract
Monkeypox (now Mpox), a zoonotic disease caused by the monkeypox virus (MPXV) is an emerging threat to global health. In the time span of only six months, from May to October 2022, the number of MPXV cases breached 80,000 and many of the outbreaks occurred in locations that had never previously reported MPXV. Currently there are no FDA-approved MPXV-specific vaccines or treatments, therefore, finding drugs to combat MPXV is of utmost importance. The A42R profilin-like protein of the MPXV is involved in cell development and motility making it a critical drug target. A42R protein is highly conserved across orthopoxviruses, thus A42R inhibitors may work for other family members. This study sought to identify potential A42R inhibitors for MPXV treatment using computational approaches. The energy minimized 3D structure of the A42R profilin-like protein (PDB ID: 4QWO) underwent virtual screening using a library of 36,366 compounds from Traditional Chinese Medicine (TCM), AfroDb, and PubChem databases as well as known inhibitor tecovirimat via AutoDock Vina. A total of seven compounds comprising PubChem CID: 11371962, ZINC000000899909, ZINC000001632866, ZINC000015151344, ZINC000013378519, ZINC000000086470, and ZINC000095486204, predicted to have favorable binding were shortlisted. Molecular docking suggested that all seven proposed compounds have higher binding affinities to A42R (-7.2 to -8.3 kcal/mol) than tecovirimat (-6.7 kcal/mol). This was corroborated by MM/PBSA calculations, with tecovirimat demonstrating the highest binding free energy of -68.694 kJ/mol (lowest binding affinity) compared to the seven shortlisted compounds that ranged from -73.252 to -97.140 kJ/mol. Furthermore, the 7 compounds in complex with A42R demonstrated higher stability than the A42R-tecovirimat complex when subjected to 100 ns molecular dynamics simulations. The protein-ligand interaction maps generated using LigPlot+ suggested that residues Met1, Glu3, Trp4, Ile7, Arg127, Val128, Thr131, and Asn133 are important for binding. These seven compounds were adequately profiled to be potential antivirals via PASS predictions and structural similarity searches. All seven potential lead compounds were scored Pa > Pi for antiviral activity while ZINC000001632866 and ZINC000015151344 were predicted as poxvirus inhibitors with Pa values of 0.315 and 0.215, and Pi values of 0.052 and 0.136, respectively. Further experimental validations of the identified lead compounds are required to corroborate their predicted activity. These seven identified compounds represent solid footing for development of antivirals against MPXV and other orthopoxviruses.
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Affiliation(s)
- Carolyn N. Ashley
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL, United States
| | - Emmanuel Broni
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL, United States
| | - Chanyah M. Wood
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL, United States
- Department of Chemistry and Physics, Lincoln University, Lincoln, PA, United States
| | - Tunmise Okuneye
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL, United States
- Department of Biology, Lincoln University, Lincoln, PA, United States
| | - Mary-Pearl T. Ojukwu
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL, United States
- Department of Chemistry and Physics, Lincoln University, Lincoln, PA, United States
- College of Pharmacy, University of Florida, Orlando, FL, United States
| | - Qunfeng Dong
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL, United States
- Center for Biomedical Informatics, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States
| | - Carla Gallagher
- Department of Chemistry and Physics, Lincoln University, Lincoln, PA, United States
| | - Whelton A. Miller
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL, United States
- Department of Molecular Pharmacology & Neuroscience, Loyola University Medical Center, Loyola University Chicago, Maywood, IL, United States
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Moetlediwa MT, Jack BU, Mazibuko-Mbeje SE, Pheiffer C, Titinchi SJJ, Salifu EY, Ramharack P. Evaluating the Therapeutic Potential of Curcumin and Synthetic Derivatives: A Computational Approach to Anti-Obesity Treatments. Int J Mol Sci 2024; 25:2603. [PMID: 38473849 DOI: 10.3390/ijms25052603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/30/2024] [Accepted: 02/09/2024] [Indexed: 03/14/2024] Open
Abstract
Natural compounds such as curcumin, a polyphenolic compound derived from the rhizome of turmeric, have gathered remarkable scientific interest due to their diverse metabolic benefits including anti-obesity potential. However, curcumin faces challenges stemming from its unfavorable pharmacokinetic profile. To address this issue, synthetic curcumin derivatives aimed at enhancing the biological efficacy of curcumin have previously been developed. In silico modelling techniques have gained significant recognition in screening synthetic compounds as drug candidates. Therefore, the primary objective of this study was to assess the pharmacokinetic and pharmacodynamic characteristics of three synthetic derivatives of curcumin. This evaluation was conducted in comparison to curcumin, with a specific emphasis on examining their impact on adipogenesis, inflammation, and lipid metabolism as potential therapeutic targets of obesity mechanisms. In this study, predictive toxicity screening confirmed the safety of curcumin, with the curcumin derivatives demonstrating a safe profile based on their LD50 values. The synthetic curcumin derivative 1A8 exhibited inactivity across all selected toxicity endpoints. Furthermore, these compounds were deemed viable candidate drugs as they adhered to Lipinski's rules and exhibited favorable metabolic profiles. Molecular docking studies revealed that both curcumin and its synthetic derivatives exhibited favorable binding scores, whilst molecular dynamic simulations showed stable binding with peroxisome proliferator-activated receptor gamma (PPARγ), csyclooxygenase-2 (COX2), and fatty acid synthase (FAS) proteins. The binding free energy calculations indicated that curcumin displayed potential as a strong regulator of PPARγ (-60.2 ± 0.4 kcal/mol) and FAS (-37.9 ± 0.3 kcal/mol), whereas 1A8 demonstrated robust binding affinity with COX2 (-64.9 ± 0.2 kcal/mol). In conclusion, the results from this study suggest that the three synthetic curcumin derivatives have similar molecular interactions to curcumin with selected biological targets. However, in vitro and in vivo experimental studies are recommended to validate these findings.
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Affiliation(s)
- Marakiya T Moetlediwa
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg 7505, South Africa
- Department of Biochemistry, North-West University, Mmabatho 2745, South Africa
| | - Babalwa U Jack
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg 7505, South Africa
| | | | - Carmen Pheiffer
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg 7505, South Africa
- Department of Obstetrics and Gynaecology, Faculty of Health Sciences, University of Pretoria, Pretoria 0001, South Africa
| | - Salam J J Titinchi
- Department of Chemistry, Faculty of Natural Science, University of the Western Cape, Bellville 7535, South Africa
| | - Elliasu Y Salifu
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg 7505, South Africa
| | - Pritika Ramharack
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg 7505, South Africa
- Pharmaceutical Sciences, School of Health Sciences, University of KwaZulu-Natal, Westville, Durban 4001, South Africa
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43
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Jawarkar RD, Zaki MEA, Al-Hussain SA, Al-Mutairi AA, Samad A, Masand V, Humane V, Mali S, Alzahrani AYA, Rashid S, Elossaily GM. Mechanistic QSAR modeling derived virtual screening, drug repurposing, ADMET and in- vitro evaluation to identify anticancer lead as lysine-specific demethylase 5a inhibitor. J Biomol Struct Dyn 2024:1-31. [PMID: 38385447 DOI: 10.1080/07391102.2024.2319104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 02/11/2024] [Indexed: 02/23/2024]
Abstract
A lysine-specific demethylase is an enzyme that selectively eliminates methyl groups from lysine residues. KDM5A, also known as JARID1A or RBP2, belongs to the KDM5 Jumonji histone demethylase subfamily. To identify novel molecules that interact with the LSD5A receptor, we created a quantitative structure-activity relationship (QSAR) model. A group of 435 compounds was used in a study of the quantitative relationship between structure and activity to guess the IC50 values for blocking LASD5A. We used a genetic algorithm-multilinear regression-based quantitative structure-activity connection model to forecast the bioactivity (PIC50) of 1615 food and drug administration pharmaceuticals from the zinc database with the goal of repurposing clinically used medications. We used molecular docking, molecular dynamic simulation modelling, and molecular mechanics generalised surface area analysis to investigate the molecule's binding mechanism. A genetic algorithm and multi-linear regression method were used to make six variable-based quantitative structure-activity relationship models that worked well (R2 = 0.8521, Q2LOO = 0.8438, and Q2LMO = 0.8414). ZINC000000538621 was found to be a new hit against LSD5A after a quantitative structure-activity relationship-based virtual screening of 1615 zinc food and drug administration compounds. The docking analysis revealed that the hit molecule 11 in the KDM5A binding pocket adopted a conformation similar to the pdb-6bh1 ligand (docking score: -8.61 kcal/mol). The results from molecular docking and the quantitative structure-activity relationship were complementary and consistent. The most active lead molecule 11, which has shown encouraging results, has good absorption, distribution, metabolism, and excretion (ADME) properties, and its toxicity has been shown to be minimal. In addition, the MTT assay of ZINC000000538621 with MCF-7 cell lines backs up the in silico studies. We used molecular mechanics generalise borne surface area analysis and a 200-ns molecular dynamics simulation to find structural motifs for KDM5A enzyme interactions. Thus, our strategy will likely expand food and drug administration molecule repurposing research to find better anticancer drugs and therapies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rahul D Jawarkar
- Department of Medicinal Chemistry and Drug discovery, Dr. Rajendra Gode Institute of Pharmacy, Amravati, Maharashtra, India
| | - Magdi E A Zaki
- Department of Chemistry, Faculty of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Sami A Al-Hussain
- Department of Chemistry, Faculty of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Aamal A Al-Mutairi
- Department of Chemistry, Faculty of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Abdul Samad
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tishk International University, Erbil, Kurdistan Region, Iraq
| | - Vijay Masand
- Department of Chemistry, Amravati, Maharashtra, India
| | - Vivek Humane
- Department of Chemistry, Shri R. R. Lahoti Science college, Morshi District: Amravati, Maharashtra, India
| | - Suraj Mali
- School of Pharmacy, D.Y. Patil University (Deemed to be University), Nerul, Navi Mumbai, India
| | | | - Summya Rashid
- Department of Pharmacology & Toxicology, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Gehan M Elossaily
- Department of Basic Medical Sciences, College of Medicine, AlMaarefa University, Riyadh, Saudi Arabia
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Yu D, Du J, He P, Wang N, Li L, Liu Y, Yang C, Xu H, Li Y. Identification of natural xanthine oxidase inhibitors: Virtual screening, anti-xanthine oxidase activity, and interaction mechanism. Int J Biol Macromol 2024; 259:129286. [PMID: 38216015 DOI: 10.1016/j.ijbiomac.2024.129286] [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: 09/05/2023] [Revised: 01/04/2024] [Accepted: 01/04/2024] [Indexed: 01/14/2024]
Abstract
Xanthine oxidase (XO) is a crucial target for hyperuricemia treatment(s). Naturally occurred XO inhibitors with minimal toxicity and high efficacy have attracted researchers' attention. With the goal of quickly identifying natural XO inhibitors, an integrated computational screening strategy was constructed by molecular docking and calculating the free energy of binding. Twenty-seven hits were achieved from a database containing 19,377 natural molecules. This includes fourteen known XO inhibitors and four firstly-reported inhibitors (isolicoflavonol, 5,7-dihydroxycoumarin, parvifolol D and clauszoline M, IC50 < 40 μM). Iolicoflavonol (hit 8, IC50 = 8.45 ± 0.68 μM) and 5,7-dihydroxycoumarin (hit 25, IC50 = 10.91 ± 0.71 μM) displayed the great potency as mixed-type inhibitors. Docking study and molecular dynamics simulation revealed that both hits could interact with XO's primarily active site residues ARG880, MOS1328, and ASN768 of XO. Fluorescence spectroscopy studies showed that hit 8 bound to the active cavity region of XO, causing changes in XO's conformation and hydrophobicity. Hits 8 and 25 exhibit favorable Absorption, Distribution, Metabolism, and Excretion (ADME) properties. Additionally, no cytotoxicity against human liver cells was observed at their median inhibition concentrations against XO. Therefore, the present study offers isolicoflavonol and 5,7-dihydroxycoumarin with the potential to be disease-modifying agents for hyperuricemia.
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Affiliation(s)
- Dehong Yu
- School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Jiana Du
- School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Pei He
- School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Na Wang
- School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Lizi Li
- School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Yi Liu
- School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Can Yang
- School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Haiqi Xu
- School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Yanfang Li
- School of Chemical Engineering, Sichuan University, Chengdu 610065, China.
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45
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Mahmood Janlou MA, Sahebjamee H, Yazdani M, Fozouni L. Structure-based virtual screening and molecular dynamics approaches to identify new inhibitors of Staphylococcus aureus sortase A. J Biomol Struct Dyn 2024; 42:1157-1169. [PMID: 37184111 DOI: 10.1080/07391102.2023.2201863] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 03/28/2023] [Indexed: 05/16/2023]
Abstract
Staphylococcus aureus is a prevalent Gram-positive bacteria leading cause of a wide range of human pathologies. Moreover, antibiotic résistance of pathogenesis bacteria is one of the worldwide health problems. In Gram-positive bacteria, the enzyme of SrtA, is responsible for the anchoring of surface-exposed proteins to the cell wall peptidoglycan. Because of its critical role in Gram-positive bacterial pathogenesis, SrtA is an attractive target for anti-virulence during drug development. To date, some SrtA inhibitors have been discovered most of them being derived from flavonoid compounds, like Myricetin. In order to provide potential hit molecules against SrtA for clinical use, we obtained a total of 293 compounds by performing in silico shape-based screening of compound libraries against Myristin as a reference structure. Employing molecular docking and scoring functions, the top 3 compounds Apigenin, Efloxate, and Compound 8261032 were screened by comparing their docking scores with Myricetin. Furthermore, MD simulations and MM-PBSA binding energy calculation studies revealed that only Compound 8261032 strongly binds to the catalytic core of the SrtA enzyme than Myricetin, and stable behavior was consistently observed in the docking complex. Compound 8261032 showed a good number of hydrogen bonds with SrtA and higher MM-PBSA binding energy when compared to all three molecules. Also, it makes strength interactions with Arg139 and His62, which are critical for SrtA biological activity. This study showed that the development of this inhibitor could be a fundamental strategy against resistant bacteria, but further studies in vitro are needed to confirm this claim.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mehr Ali Mahmood Janlou
- Department of Biophysics, Faculty of Biological Sciences, Gorgan Branch, Islamic Azad University, Gorgan, Iran
| | - Hassan Sahebjamee
- Department of Biophysics, Faculty of Biological Science, Varamin-Pishva Branch, Islamic Azad University, Varamin, Iran
| | - Mohsen Yazdani
- Laboratory of Bioinformatics and Drug Design, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Leila Fozouni
- Department of Microbiology, Faculty of Biological Sciences, Gorgan Branch, Islamic Azad University, Gorgan, Iran
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46
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Azhagesan A, Rajendran D, Varghese RP, George Priya Doss C, Chandrasekaran N. Assessment of polystyrene nano plastics effect on human salivary α-amylase structural alteration: Insights from an in vitro and in silico study. Int J Biol Macromol 2024; 257:128650. [PMID: 38065455 DOI: 10.1016/j.ijbiomac.2023.128650] [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: 08/16/2023] [Revised: 11/19/2023] [Accepted: 12/05/2023] [Indexed: 12/21/2023]
Abstract
The study found that the enzyme activity of human salivary α-amylase (α-AHS) was competitively inhibited by nanoplastic polystyrene (PS-NPs), with a half-inhibitory concentration (IC50) of 92 μg/mL, while the maximum reaction rate (Vmax) remained unchanged at 909 μg/mL•min. An increase in the concentration of PS-NPs led to a quenching of α-AHS fluorescence with a slight red shift, indicating a static mechanism. The binding constant (Ka) and quenching constant (Kq) were calculated to be 2.92 × 1011 M-1 and 1.078 × 1019 M-1• S-1 respectively, with a hill coefficient (n) close to one and an apparent binding equilibrium constant (KA) of 1.54 × 1011 M-1. Molecular docking results suggested that the interaction between α-AHS and PS-NPs involved π-anion interactions between the active site Asp197, Asp300 residues, and van der Waals force interactions affecting the Tyr, Trp, and other residues. Fourier transform infrared (FT-IR) and circular dichroism (CD) analyses revealed conformational changes in α-AHS, including a loss of secondary structure α-helix and β-sheet. The study concludes that the interaction between α-AHS and PS-NPs leads to structural and functional changes in α-AHS, potentially impacting human health. This research provides a foundation for further toxicological analysis of MPs/NPs in the human digestive system.
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Affiliation(s)
- Ananthaselvam Azhagesan
- Centre for Nanobiotechnology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu 632 014, India
| | - Durgalakshmi Rajendran
- Centre for Nanobiotechnology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu 632 014, India
| | - Rinku Polachirakkal Varghese
- Department of Integrative Biology, School of BioSciences & Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu 632 014, India
| | - C George Priya Doss
- Department of Integrative Biology, School of BioSciences & Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu 632 014, India
| | - Natarajan Chandrasekaran
- Centre for Nanobiotechnology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu 632 014, India.
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47
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Nazir A, Shad M, Rashid N, Azim N, Sajjad M. Recombinant production and characterization of a metal ion-independent Lysophospholipase from a hyperthermophilic archaeon Pyrococcus abyssi DSM25543. Int J Biol Macromol 2024; 259:129345. [PMID: 38219941 DOI: 10.1016/j.ijbiomac.2024.129345] [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: 10/22/2023] [Revised: 12/13/2023] [Accepted: 01/07/2024] [Indexed: 01/16/2024]
Abstract
Genome sequence of Pyrococcus abyssi DSM25543 contains a coding sequence (PAB_RS01410) for α/β hydrolase (WP_010867387.1). Structural analysis revealed the presence of a consensus motif GXSXG and a highly conserved catalytic triad in the amino acid sequence of α/β hydrolase that were characteristic features of lysophospholipases. A putative lysophospholipase from P. abyssi with its potential applications in oil degumming and starch processing was heterologously produced in E. coli Rosetta (DE3) pLysS in soluble form followed by its purification and characterization. The recombinant enzyme was found to be active at temperature of 40-90 °C and pH 5.5-7.0. However, the enzyme exhibited its optimum activity at 65 °C and pH 6.5. None of the metal ions (Mn2+, Mg2+, Ni2+, Cu2+, Fe2+, Co2+, Zn2+ and Ca2+) being tested had stimulatory effect on lysophospholipase activity. Km and Vmax for hydrolysis of 4-nitrophenyl butyrate were calculated to be 1 ± 0.089 mM and 1637 ± 24.434 U/mg, respectively. It is the first report on the soluble production and characterization of recombinant lysophospholipase from P. abyssi which exhibits its lipolytic activity in the absence of divalent metal ions. Broad substrate specificity, activity and stability at elevated temperatures make recombinant lysophospholipase an ideal candidate for potential industrial applications.
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Affiliation(s)
- Arshia Nazir
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Mohsin Shad
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Naeem Rashid
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Naseema Azim
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Muhammad Sajjad
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan.
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48
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Savino DF, Silva JV, da Silva Santos S, Lourenço FR, Giarolla J. How do physicochemical properties contribute to inhibitory activity of promising peptides against Zika Virus NS3 protease? J Mol Model 2024; 30:54. [PMID: 38289526 DOI: 10.1007/s00894-024-05843-1] [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: 07/11/2023] [Accepted: 01/09/2024] [Indexed: 02/01/2024]
Abstract
CONTEXT AND RESULTS Flavivirus diseases' cycles, especially Dengue and Yellow Fever, can be observed all over Brazilian territory, representing a great health concern. Additionally, there are no drugs available in therapy. In this scenario, in silico methodologies were applied to obtain physicochemical properties, as well as to better understand the ligand-biological target interaction mode of 20 previously reported NS2B/NS3 protease inhibitors of Dengue virus. Since catalytic site of flavivirus hold similarities, such as the same catalytic triad (His51, Asp75 e Ser135), the ability of this series of molecules to fit in Zika NS3 domains can be achieved. We performed an exploratory data analysis, using statistical methodologies, such as PCA (Principal Component Analysis) and HCA (Hierarchical Component Analysis), to assist the comprehension of how physicochemical properties impact the interaction observed by the docking studies, as well as to build a correlation between the respective ranked characteristics. Based on these previous studies, peptides were selected for the dynamics simulations, which were useful to better understand the ligand-protein interactions. Information relating to, for instance, energy, ΔG, average number of hydrogen bonds and distance from Ser135 (one of the main amino acids in the catalytic pocket) were discussed. In this sense, peptides 15 (considering ΔG value and Hbond number), 7 (ΔG and energy) and 1, 6, 7 and 15 (the proximity to Ser135 throughout the dynamics simulation) were highlighted as promising. Those interesting results could contribute to future studies regarding Zika virus drug design, since this infection represents a great concern in neglected populations. METHODS The models were constructed in the ChemDraw software. The ligand parametrization was performed in the CHEM3D 17.0, UCSF Chimera. Docking simulations were carried out in the GOLD software, after the redocking validation. We used ASP as the function score. Additionally, for dynamics simulations we applied GROMACS software, exploring, mainly, free binding energy calculations. Exploratory analysis was carried out in Minitab 17.3.1 statistical software. Prior to the exploratory analysis, data of quantum chemical properties of the peptides were collected in Microsoft Excel spreadsheet and organized to obtain Hierarchical Cluster Analysis (HCA) and Principal Component Analysis (PCA).
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Affiliation(s)
- Débora Feliciano Savino
- Department of Pharmacy, School of Pharmaceutical Sciences, University of São Paulo (USP), Professor Lineu Prestes Avenue, 580, Building 13, São Paulo, SP, 05508-900, Brazil
| | - João Vitor Silva
- Department of Pharmacy, School of Pharmaceutical Sciences, University of São Paulo (USP), Professor Lineu Prestes Avenue, 580, Building 13, São Paulo, SP, 05508-900, Brazil
| | - Soraya da Silva Santos
- Department of Pharmacy, School of Pharmaceutical Sciences, University of São Paulo (USP), Professor Lineu Prestes Avenue, 580, Building 13, São Paulo, SP, 05508-900, Brazil
| | - Felipe Rebello Lourenço
- Department of Pharmacy, School of Pharmaceutical Sciences, University of São Paulo (USP), Professor Lineu Prestes Avenue, 580, Building 13, São Paulo, SP, 05508-900, Brazil
| | - Jeanine Giarolla
- Department of Pharmacy, School of Pharmaceutical Sciences, University of São Paulo (USP), Professor Lineu Prestes Avenue, 580, Building 13, São Paulo, SP, 05508-900, Brazil.
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Gowtham H, Revanasiddappa PD, Murali M, Singh SB, Abhilash M, Pradeep S, Shivamallu C, Achar RR, Silina E, Stupin V, Manturova N, Shati AA, Alfaifi MY, Elbehairi SEI, Kollur SP. Secondary metabolites of Trichoderma spp. as EGFR tyrosine kinase inhibitors: Evaluation of anticancer efficacy through computational approach. PLoS One 2024; 19:e0296010. [PMID: 38266021 PMCID: PMC10824427 DOI: 10.1371/journal.pone.0296010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 12/01/2023] [Indexed: 01/26/2024] Open
Abstract
The present study explores the epidermal growth factor receptor (EGFR) tyrosine kinase inhibition efficacy of secondary metabolites in Trichoderma spp. through molecular docking, molecular dynamics (MD) simulation and MM-PBSA approach. The result of molecular docking confirmed that out of 200 metabolites screened, three metabolites such as Harzianelactone A, Pretrichodermamide G and Aspochalasin M, potentially bound with the active binding site of EGFR tyrosine kinase domain(PDB ID: 1M17) with a threshold docking score of ≤- 9.0 kcal/mol when compared with the standard EGFR inhibitor (Erlotinib). The MD simulation was run to investigate the potential for stable complex formation in EGFR tyrosine kinase domain-unbound/lead metabolite (Aspochalasin M)-bound/standard inhibitor (Erlotinib)-bound complex. The MD simulation analysis at 100 ns revealed that Aspochalasin M formed the stable complex with EGFR. Besides, the in silico predication of pharmacokinetic properties further confirmed that Aspochalasin M qualified the drug-likeness rules with no harmful side effects (viz., hERG toxicity, hepatotoxicity and skin sensitization), non-mutagenicity and favourable logBB value. Moreover, the BOILED-Egg model predicted that Aspochalasin M showed a higher gastrointestinal absorption with improved bioavailability when administered orally and removed from the central nervous system (CNS). The results of the computational studies concluded that Aspochalasin M possessed significant efficacy in binding EGFR's active sites compared to the known standard inhibitor (Erlotinib). Therefore, Aspochalasin M can be used as a possible anticancer drug candidate and further in vitro and in vivo experimental validation of Aspochalasin M of Trichoderma spp. are required to determine its anticancer potential.
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Affiliation(s)
- H.G. Gowtham
- Department of PG Studies in Biotechnology, Nrupathunga University, Bangalore, Karnataka, India
| | | | | | | | - M.R. Abhilash
- Department of Studies in Environmental Science, University of Mysore, Mysore, India
| | - Sushma Pradeep
- Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education & Research, Mysuru, Karnataka, India
| | - Chandan Shivamallu
- Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education & Research, Mysuru, Karnataka, India
| | - Raghu Ram Achar
- Division of Biochemistry, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
| | - Ekaterina Silina
- Department of Human Pathology, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Victor Stupin
- Department of Hospital Surgery, NI. Pirogov Russian National Research Medical University, Moscow, Russia
| | - Natalia Manturova
- Department of Hospital Surgery, NI. Pirogov Russian National Research Medical University, Moscow, Russia
| | - Ali A. Shati
- Biology Department, Faculty of Science, King Khalid University, Abha, Saudi Arabia
| | - Mohammad Y. Alfaifi
- Biology Department, Faculty of Science, King Khalid University, Abha, Saudi Arabia
| | | | - Shiva Prasad Kollur
- School of Physical Sciences, Amrita Vishwa Vidyapeetham, Mysuru Campus, Mysuru, Karnataka, India
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50
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Simanjuntak MV, Jauhar MM, Syaifie PH, Arda AG, Mardliyati E, Shalannanda W, Hermanto BR, Anshori I. Revealing Propolis Potential Activity on Inhibiting Estrogen Receptor and Heat Shock Protein 90 Overexpressed in Breast Cancer by Bioinformatics Approaches. Bioinform Biol Insights 2024; 18:11779322231224187. [PMID: 38274992 PMCID: PMC10809879 DOI: 10.1177/11779322231224187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 12/15/2023] [Indexed: 01/27/2024] Open
Abstract
Breast cancer is the most commonly diagnosed cancer globally, with the highest incidence of breast cancer occurring in Asian countries including Indonesia. Among the types of breast cancer, the estrogen receptor (ER)-positive subtype which is prominent with estrogen receptor alpha (ERα) and heat shock protein 90 (HSP90) overexpression genes becomes the most prevalent than the others, approximately 75% of all breast cancer cases. ERα and HSP90 play a role in breast cancer activities including breast tumor growth, invasion, and metastasis mechanism. Propolis, a natural bee product, has been explored for its anticancer activity. However, there is lack of studies that evaluated the potential inhibitor from propolis compounds to the ERα and HSP90 proteins. Therefore, this article focuses on examining the correlation between ERα and HSP90's role in breast cancer and investigating the potential of 93 unique propolis compositions in inhibiting these genes in breast cancer using in silico approaches. This study revealed the positive correlation between ERα and HSP90 genes in breast cancer disease development. Furthermore, we also found novel potential bioactive compounds of propolis against breast cancer through binding with ERα and HSP90; they were 3',4',7-trihydroxyisoflavone and baicalein-7-O-β-D glucopyranoside, respectively. Further research on these compounds is needed to elucidate deeper mechanisms and activity in the real biological system to develop new breast cancer drug treatments.
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Affiliation(s)
- Masriana Vivi Simanjuntak
- Biomedical Engineering Department, School of Electrical Engineering and Informatics, Bandung Institute of Technology, Bandung, Indonesia
| | - Muhammad Miftah Jauhar
- Center of Excellences Life Sciences, Nano Center Indonesia, South Tangerang, Indonesia
- Biomedical Engineering, The Graduate School of Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Putri Hawa Syaifie
- Center of Excellences Life Sciences, Nano Center Indonesia, South Tangerang, Indonesia
| | - Adzani Gaisani Arda
- Center of Excellences Life Sciences, Nano Center Indonesia, South Tangerang, Indonesia
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Etik Mardliyati
- Research Center for Vaccine and Drug, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| | - Wervyan Shalannanda
- Biomedical Engineering Department, School of Electrical Engineering and Informatics, Bandung Institute of Technology, Bandung, Indonesia
| | - Beni Rio Hermanto
- Biomedical Engineering Department, School of Electrical Engineering and Informatics, Bandung Institute of Technology, Bandung, Indonesia
| | - Isa Anshori
- Biomedical Engineering Department, School of Electrical Engineering and Informatics, Bandung Institute of Technology, Bandung, Indonesia
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