1
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Dulay ANG, de Guzman JCC, Marquez ZYD, Santana ESD, Arce J, Orosco FL. The potential of Chlorella spp. as antiviral source against African swine fever virus through a virtual screening pipeline. J Mol Graph Model 2024; 132:108846. [PMID: 39151375 DOI: 10.1016/j.jmgm.2024.108846] [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: 04/01/2024] [Revised: 06/26/2024] [Accepted: 08/02/2024] [Indexed: 08/19/2024]
Abstract
African swine fever (ASF) causes high mortality in pigs and threatens global swine production. There is still a lack of therapeutics available, with two vaccines under scrutiny and no approved small-molecule drugs. Eleven (11) viral proteins were used to identify potential antivirals in in silico screening of secondary metabolites (127) from Chlorella spp. The metabolites were screened for affinity and binding selectivity. High-scoring compounds were assessed through in silico ADMET (Absorption, Distribution, Metabolism, Excretion, Toxicity) predictions, compared to structurally similar drugs, and checked for off-target docking with prepared swine receptors. Molecular dynamics (MD) simulations determined binding stability while binding energy was measured in Molecular Mechanics - Generalized Born Surface Area (MMGBSA) or Poisson-Boltzmann Surface Area (MMPBSA). Only six (6) compounds passed until MD analyses, of which five (5) were stable after 100 ns of MD runs. Of these five compounds, only three had binding affinities that were comparable to or stronger than controls. Specifically, phytosterols 24,25-dihydrolanosterol and CID 4206521 that interact with the RNA capping enzyme (pNP868R), and ergosterol which bound to the Erv-like thioreductase (pB119L). The compounds identified in this study can be used as a theoretical basis for in vitro screening to develop potent antiviral drugs against ASFV.
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Affiliation(s)
- Albert Neil G Dulay
- Virology and Vaccine Research Program, Industrial Technology Development Institute, Department of Science and Technology, Taguig, 1632, Philippines
| | - John Christian C de Guzman
- Virology and Vaccine Research Program, Industrial Technology Development Institute, Department of Science and Technology, Taguig, 1632, Philippines
| | - Zyra Ysha D Marquez
- Department of Biology, College of Arts and Sciences, University of the Philippines - Manila, Manila, 1000, Philippines
| | - Elisha Sofia D Santana
- Department of Biology, College of Arts and Sciences, University of the Philippines - Manila, Manila, 1000, Philippines
| | - Jessamine Arce
- Department of Biology, College of Arts and Sciences, University of the Philippines - Manila, Manila, 1000, Philippines
| | - Fredmoore L Orosco
- Virology and Vaccine Research Program, Industrial Technology Development Institute, Department of Science and Technology, Taguig, 1632, Philippines; Department of Biology, College of Arts and Sciences, University of the Philippines - Manila, Manila, 1000, Philippines; S&T Fellows Program, Department of Science and Technology, Taguig, 1632, Philippines.
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2
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Zondagh LS, Malan SF, Joubert J. Edaravone N-benzyl pyridinium derivatives: BACE-1 inhibition, kinetics and in silico binding pose determination. Eur J Pharm Sci 2024; 201:106869. [PMID: 39102997 DOI: 10.1016/j.ejps.2024.106869] [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: 05/24/2024] [Revised: 07/08/2024] [Accepted: 08/02/2024] [Indexed: 08/07/2024]
Abstract
BACE-1 plays a pivotal role in the production of β-amyloid (Aβ) peptides, implicated in Alzheimer's Disease (AD) pathology. We previously described edaravone N-benzyl pyridinium derivatives (EBPDs) that exhibited multifunctional activity against multiple AD targets. In this study we explored the EBPDs BACE-1 inhibitory activity to potentially enhance the compounds therapeutic profile. The EBPDs exhibited moderate BACE-1 inhibitory activity (IC50 = 44.10 µM - 123.70 µM) and obtained IC50 values between 2.0 and 5.8-fold greater than resveratrol, a known BACE-1 inhibitor (IC50 = 253.20 µM), in this assay. Compound 3 was the most potent inhibitor with an IC50 of 44.10 µM and a Ki of 19.96 µM and a mixed-type mode of inhibition that favored binding in a competitive manner. Molecular docking identified crucial interactions with BACE-1 active site residues, supported by 100 ns MD simulations. The study highlighted the EBPDs therapeutic potential as BACE-1 inhibitors and multifunctional anti-AD therapeutic agents.
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Affiliation(s)
- L S Zondagh
- Pharmaceutical Chemistry, School of Pharmacy, University of the Western Cape, Cape Town, Western Cape 7535, South Africa
| | - S F Malan
- Pharmaceutical Chemistry, School of Pharmacy, University of the Western Cape, Cape Town, Western Cape 7535, South Africa
| | - J Joubert
- Pharmaceutical Chemistry, School of Pharmacy, University of the Western Cape, Cape Town, Western Cape 7535, South Africa.
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3
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Paterson LC, Humphreys PG, Kelly HA, Kerr WJ. Collaborative GSK-University of Strathclyde doctoral research and training programmes: Transforming approaches to industry-academia engagement. Drug Discov Today 2024:104162. [PMID: 39245346 DOI: 10.1016/j.drudis.2024.104162] [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: 07/18/2024] [Revised: 08/23/2024] [Accepted: 09/05/2024] [Indexed: 09/10/2024]
Abstract
A global biopharma company, GSK, and the University of Strathclyde have developed an expansive and transformative research and training partnership originating in chemistry-aligned disciplines, with subsequent extensive expansion across further areas of the company. This has opened unique approaches for the delivery of collaborative research innovations while also enhancing the professional development and learning of GSK personnel, in addition to other embedded researchers and collaborating scientists, on a pathway towards more rapid and efficient discovery of new medicines.
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Affiliation(s)
- Laura C Paterson
- University of Strathclyde, Pure and Applied Chemistry, 295 Cathedral Street, Glasgow G1 1XL, UK
| | | | - Henry A Kelly
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, UK.
| | - William J Kerr
- University of Strathclyde, Pure and Applied Chemistry, 295 Cathedral Street, Glasgow G1 1XL, UK.
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4
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Qiao K, Xu C, Zhang C, Wang Q, Jiang J, Chen Z, Zhou L, Jia S, Cao L. Discovery of an 8-oxoguanine regulator PCBP1 inhibitor by virtual screening and its synergistic effects with ROS-modulating agents in pancreatic cancer. Front Mol Biosci 2024; 11:1441550. [PMID: 39170746 PMCID: PMC11336162 DOI: 10.3389/fmolb.2024.1441550] [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: 05/31/2024] [Accepted: 07/24/2024] [Indexed: 08/23/2024] Open
Abstract
Introduction: Drugs that target reactive oxygen species (ROS) metabolism have progressed the treatment of pancreatic cancer treatment, yet their efficacy remains poor because of the adaptation of cancer cells to high concentration of ROS. Cells cope with ROS by recognizing 8-oxoguanine residues and processing severely oxidized RNA, which make it feasible to improve the efficacy of ROS-modulating drugs in pancreatic cancer by targeting 8-oxoguanine regulators. Methods: Poly(rC)-binding protein 1 (PCBP1) was identified as a potential oncogene in pancreatic cancer through datasets of The Cancer Genome Atlas (TCGA) project and Gene Expression Omnibus (GEO). High-throughput virtual screening was used to screen out potential inhibitors for PCBP1. Computational molecular dynamics simulations was used to verify the stable interaction between the two compounds and PCBP1 and their structure-activity relationships. In vitro experiments were performed for functional validation of silychristin. Results: In this study, we identified PCBP1 as a potential oncogene in pancreatic cancer. By applying high-throughput virtual screening, we identified Compound 102 and Compound 934 (silychristin) as potential PCBP1 inhibitors. Computational molecular dynamics simulations and virtual alanine mutagenesis verified the structure-activity correlation between PCBP1 and the two identified compounds. These two compounds interfere with the PCBP1-RNA interaction and impair the ability of PCBP1 to process RNA, leading to intracellular R loop accumulation. Compound 934 synergized with ROS agent hydrogen peroxide to strongly improve induced cell death in pancreatic cancer cells. Discussion: Our results provide valuable insights into the development of drugs that target PCBP1 and identified promising synergistic agents for ROS-modulating drugs in pancreatic cancer.
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Affiliation(s)
- Kexiong Qiao
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Chengjie Xu
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Chaolei Zhang
- Department of Emergency Medicine, Sir Run Run Shaw Hospital, Hangzhou, Zhejiang Province, China
| | - Qianqian Wang
- School of Medicine, Sir Run Run Shaw Hospital, Graduate School, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jun Jiang
- School of Medicine, Sir Run Run Shaw Hospital, Graduate School, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zongrong Chen
- School of Medicine, Sir Run Run Shaw Hospital, Graduate School, Zhejiang University, Hangzhou, Zhejiang, China
| | - Liangjing Zhou
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Shengnan Jia
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Liping Cao
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
- Zhejiang Engineering Research Center of Cognitive Healthcare, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine,, Hangzhou, Zhejiang Province, China
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5
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Yau MQ, Wan AJ, Tiong ASH, Yiap YS, Loo JSE. Leveraging binding pose metadynamics to optimise target fishing predictions for three diverse ligands and their true targets. Chem Biol Drug Des 2024; 104:e14591. [PMID: 39010276 DOI: 10.1111/cbdd.14591] [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: 02/11/2024] [Revised: 04/08/2024] [Accepted: 07/09/2024] [Indexed: 07/17/2024]
Abstract
Computational target fishing plays an important role in target identification, particularly in drug discovery campaigns utilizing phenotypic screening. Numerous approaches exist to predict potential targets for a given ligand, but true targets may be inconsistently ranked. More advanced simulation methods may provide benefit in such cases by reranking these initial predictions. We evaluated the ability of binding pose metadynamics to improve the predicted rankings for three diverse ligands and their six true targets. Initial predictions using pharmacophore mapping showed no true targets ranked in the top 50 and two targets each ranked within the 50-100, 100-150, and 250-300 ranges respectively. Following binding pose metadynamics, ranking of true targets improved for four out of the six targets and included the highest ranked predictions overall, while rankings deteriorated for two targets. The revised rankings predicted two true targets ranked within the top 50, and one target each within the 50-100, 100-150, 150-200, and 200-250 ranges respectively. The findings of this study demonstrate that binding pose metadynamics may be of benefit in refining initial predictions from structure-based target fishing algorithms, thereby improving the efficiency of the target identification process in drug discovery efforts.
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Affiliation(s)
- Mei Qian Yau
- School of Pharmacy, Faculty of Health & Medical Sciences, Taylor's University, Subang Jaya, Selangor, Malaysia
- Digital Health and Medical Advancement Impact Lab, Taylor's University, Subang Jaya, Selangor, Malaysia
| | - Angeline J Wan
- School of Pharmacy, Faculty of Health & Medical Sciences, Taylor's University, Subang Jaya, Selangor, Malaysia
| | - Aaron S H Tiong
- School of Pharmacy, Faculty of Health & Medical Sciences, Taylor's University, Subang Jaya, Selangor, Malaysia
| | - Yong Sheng Yiap
- School of Pharmacy, Faculty of Health & Medical Sciences, Taylor's University, Subang Jaya, Selangor, Malaysia
| | - Jason S E Loo
- School of Pharmacy, Faculty of Health & Medical Sciences, Taylor's University, Subang Jaya, Selangor, Malaysia
- Digital Health and Medical Advancement Impact Lab, Taylor's University, Subang Jaya, Selangor, Malaysia
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6
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Shen Z, Xu L, Wu T, Wang H, Wang Q, Ge X, Kong F, Huang G, Pan X. Structural basis for urate recognition and apigenin inhibition of human GLUT9. Nat Commun 2024; 15:5039. [PMID: 38866775 PMCID: PMC11169512 DOI: 10.1038/s41467-024-49420-9] [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: 01/18/2024] [Accepted: 06/03/2024] [Indexed: 06/14/2024] Open
Abstract
Urate, the physiological form of uric acid and a potent antioxidant in serum, plays a pivotal role in scavenging reactive oxygen species. Yet excessive accumulation of urate, known as hyperuricemia, is the primary risk factor for the development of gout. The high-capacity urate transporter GLUT9 represents a promising target for gout treatment. Here, we present cryo-electron microscopy structures of human GLUT9 in complex with urate or its inhibitor apigenin at overall resolutions of 3.5 Å and 3.3 Å, respectively. In both structures, GLUT9 exhibits an inward open conformation, wherein the substrate binding pocket faces the intracellular side. These structures unveil the molecular basis for GLUT9's substrate preference of urate over glucose, and show that apigenin acts as a competitive inhibitor by occupying the substrate binding site. Our findings provide critical information for the development of specific inhibitors targeting GLUT9 as potential therapeutics for gout and hyperuricemia.
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Affiliation(s)
- Zilin Shen
- Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Li Xu
- Institute of Bio-Architecture and Bio-Interactions (IBABI), Shenzhen Medical Academy of Research and Translation (SMART), Shenzhen, 518107, Guangdong, China
| | - Tong Wu
- Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Huan Wang
- Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Qifan Wang
- Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Xiaofei Ge
- Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Fang Kong
- Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Gaoxingyu Huang
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, 310024, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, 310024, Zhejiang, China
| | - Xiaojing Pan
- Institute of Bio-Architecture and Bio-Interactions (IBABI), Shenzhen Medical Academy of Research and Translation (SMART), Shenzhen, 518107, Guangdong, China.
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7
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Zeng Q, Hu H, Huang Z, Guo A, Lu S, Tong W, Zhang Z, Shen T. Active and machine learning-enhanced discovery of new FGFR3 inhibitor, Rhapontin, through virtual screening of receptor structures and anti-cancer activity assessment. Front Mol Biosci 2024; 11:1413214. [PMID: 38919748 PMCID: PMC11196408 DOI: 10.3389/fmolb.2024.1413214] [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: 04/19/2024] [Accepted: 05/23/2024] [Indexed: 06/27/2024] Open
Abstract
Introduction: This study bridges traditional remedies and modern pharmacology by exploring the synergy between natural compounds and Ceritinib in treating Non-Small Cell Lung Cancer (NSCLC), aiming to enhance efficacy and reduce toxicities. Methods: Using a combined approach of computational analysis, machine learning, and experimental procedures, we identified and analyzed PD173074, Isoquercitrin, and Rhapontin as potential inhibitors of fibroblast growth factor receptor 3 (FGFR3). Machine learning algorithms guided the initial selection, followed by Quantitative Structure-Activity Relationship (QSAR) modeling and molecular dynamics simulations to evaluate the interaction dynamics and stability of Rhapontin. Physicochemical assessments further verified its drug-like properties and specificity. Results: Our experiments demonstrate that Rhapontin, when combined with Ceritinib, significantly suppresses tumor activity in NSCLC while sparing healthy cells. The molecular simulations and physicochemical evaluations confirm Rhapontin's stability and favorable interaction with FGFR3, highlighting its potential as an effective adjunct in NSCLC therapy. Discussion: The integration of natural compounds with established cancer therapies offers a promising avenue for enhancing treatment outcomes in NSCLC. By combining the ancient wisdom of natural remedies with the precision of modern science, this study contributes to evolving cancer treatment paradigms, potentially mitigating the side effects associated with current therapies.
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Affiliation(s)
- Qingxin Zeng
- Department of Thoracic Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Haichuan Hu
- Department of Thoracic Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhengwei Huang
- Department of Thoracic Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Aotian Guo
- Department of Thoracic Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Sheng Lu
- Department of Thoracic Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Wenbin Tong
- Department of Thoracic Surgery, Longyou County People’s Hospital, Hangzhou, China
| | - Zhongheng Zhang
- Department of Emergency Medicine, Sir Run Run Shaw Hospital, Hangzhou, China
| | - Tao Shen
- Department of Thoracic Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
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8
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Lan N, Su Y, Zeng Q, Zhou P, Hu Y, Zhang Z, Wang Y, Liu K. JD-02, a novel Hsp90 inhibitor, induces ROS/SRC axis-dependent cytoprotective autophagy in colorectal cancer cells. Mol Carcinog 2024; 63:1038-1050. [PMID: 38411361 DOI: 10.1002/mc.23706] [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: 10/03/2023] [Revised: 12/09/2023] [Accepted: 02/08/2024] [Indexed: 02/28/2024]
Abstract
Heat shock protein 90 (Hsp90) is a tumor marker that accelerates cancer growth by disrupting protein homeostasis. However, concerns such as low clinical efficacy and drug resistance continue to be obstacles to the successful marketing of Hsp90 inhibitors. The cytoprotective function of autophagy has been identified as one of the mechanisms by which tumor cells gain resistance to chemotherapy. JD-02 was identified as a new Hsp90 inhibitor that suppressed colorectal cancer (CRC) growth by lowering client protein levels in vivo and in vitro. We found that JD-02 increased cellular autophagy, which inhibited apoptosis. JD-02 enhanced cytoprotective autophagy and regulated apoptotic suppression by increasing intracellular reactive oxygen species and inhibiting SRC protein levels, as demonstrated by quantitative proteomics, bioinformatic analysis, western blotting, and flow cytometry. This effect was reversed by autophagy inhibition. Therefore, due to the synergistic effects of Hsp90 and autophagy inhibitors in efficiently activating apoptotic pathways, they could potentially serve as promising therapeutic options for CRC.
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Affiliation(s)
- Ni Lan
- Guangdong Provincial Clinical Research Center for Geriatrics, Shenzhen Clinical Research Center for Geriatrics, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University, Shenzhen, China
- Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Yuan Su
- Guangdong Provincial Clinical Research Center for Geriatrics, Shenzhen Clinical Research Center for Geriatrics, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University, Shenzhen, China
- Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Qiongzhen Zeng
- Guangdong Provincial Clinical Research Center for Geriatrics, Shenzhen Clinical Research Center for Geriatrics, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University, Shenzhen, China
- Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Pengjun Zhou
- Guangdong Provincial Engineering Center of Topical Precise Drug Delivery System, School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, China
| | - Yuze Hu
- College of Pharmacy, Jinan University, Guangzhou, China
| | - Zhuo Zhang
- Guangdong Provincial Clinical Research Center for Geriatrics, Shenzhen Clinical Research Center for Geriatrics, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University, Shenzhen, China
- Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou, China
- College of Pharmacy, Jinan University, Guangzhou, China
| | - Yifei Wang
- Guangdong Provincial Clinical Research Center for Geriatrics, Shenzhen Clinical Research Center for Geriatrics, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University, Shenzhen, China
- Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou, China
- College of Pharmacy, Jinan University, Guangzhou, China
| | - Kaisheng Liu
- Guangdong Provincial Clinical Research Center for Geriatrics, Shenzhen Clinical Research Center for Geriatrics, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University, Shenzhen, China
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9
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Zhang S, Gu L, Lin Y, Zeng H, Ding N, Wei J, Gu X, Liu C, Sun W, Zhou Y, Zhang Y, Hu Z. Chaetoxylariones A-G: undescribed chromone-derived polyketides from co-culture of Chaetomium virescens and Xylaria grammica enabled via the molecular networking strategy. Bioorg Chem 2024; 147:107329. [PMID: 38608410 DOI: 10.1016/j.bioorg.2024.107329] [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: 01/03/2024] [Revised: 03/28/2024] [Accepted: 04/01/2024] [Indexed: 04/14/2024]
Abstract
By co-culturing two endophytic fungi (Chaetomium virescens and Xylaria grammica) collected from the medicinal and edible plant Smilax glabra Roxb. and analyzing them with MolNetEnhancer module on GNPS platform, seven undescribed chromone-derived polyketides (chaetoxylariones A-G), including three pairs of enantiomer ones (2a/2b, 4a/4b and 6a/6b) and four optical pure ones (1, 3, 5 and 7), as well as five known structural analogues (8-12), were obtained. The structures of these new compounds were characterized by NMR spectroscopy, single-crystal X-ray diffraction, 13C NMR calculation and DP4+ probability analyses, as well as the comparison of the experimental electronic circular dichroism (ECD) data. Structurally, compound 1 featured an unprecedented chromone-derived sulfonamide tailored by two isoleucine-derived δ-hydroxy-3-methylpentenoic acids via the acylamide and NO bonds, respectively; compound 2 represented the first example of enantiomeric chromone derivative bearing a unique spiro-[3.3]alkane ring system; compound 3 featured a decane alkyl side chain that formed an undescribed five-membered lactone ring between C-7' and C-10'; compound 4 contained an unexpected highly oxidized five-membered carbocyclic system featuring rare adjacent keto groups; compound 7 featured a rare methylsulfonyl moiety. In addition, compound 10 showed a significant inhibition towards SW620/AD300 cells with an IC50 value of PTX significantly decreased from 4.09 μM to 120 nM, and a further study uncovered that compound 10 could obviously reverse the MDR of SW620/AD300 cells.
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Affiliation(s)
- Sitian Zhang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
| | - Lianghu Gu
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
| | - Yongtong Lin
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
| | - Hanxiao Zeng
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
| | - Nanjin Ding
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
| | - Jiangchun Wei
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
| | - Xiaoxia Gu
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
| | - Chang Liu
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
| | - Weiguang Sun
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
| | - Yuan Zhou
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China.
| | - Yonghui Zhang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China.
| | - Zhengxi Hu
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China.
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10
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Stadler KA, Ortiz-Joya LJ, Singh Sahrawat A, Buhlheller C, Gruber K, Pavkov-Keller T, O'Hagan TB, Guarné A, Pulido S, Marín-Villa M, Zangger K, Gubensäk N. Structural investigation of Trypanosoma cruzi Akt-like kinase as drug target against Chagas disease. Sci Rep 2024; 14:10039. [PMID: 38693166 PMCID: PMC11063076 DOI: 10.1038/s41598-024-59654-8] [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: 01/19/2024] [Accepted: 04/12/2024] [Indexed: 05/03/2024] Open
Abstract
According to the World Health Organization, Chagas disease (CD) is the most prevalent poverty-promoting neglected tropical disease. Alarmingly, climate change is accelerating the geographical spreading of CD causative parasite, Trypanosoma cruzi, which additionally increases infection rates. Still, CD treatment remains challenging due to a lack of safe and efficient drugs. In this work, we analyze the viability of T. cruzi Akt-like kinase (TcAkt) as drug target against CD including primary structural and functional information about a parasitic Akt protein. Nuclear Magnetic Resonance derived information in combination with Molecular Dynamics simulations offer detailed insights into structural properties of the pleckstrin homology (PH) domain of TcAkt and its binding to phosphatidylinositol phosphate ligands (PIP). Experimental data combined with Alpha Fold proposes a model for the mechanism of action of TcAkt involving a PIP-induced disruption of the intramolecular interface between the kinase and the PH domain resulting in an open conformation enabling TcAkt kinase activity. Further docking experiments reveal that TcAkt is recognized by human inhibitors PIT-1 and capivasertib, and TcAkt inhibition by UBMC-4 and UBMC-6 is achieved via binding to TcAkt kinase domain. Our in-depth structural analysis of TcAkt reveals potential sites for drug development against CD, located at activity essential regions.
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Affiliation(s)
- Karina A Stadler
- Institute of Chemistry/Organic and Bioorganic Chemistry, University of Graz, Graz, Austria
| | - Lesly J Ortiz-Joya
- Institute of Chemistry/Organic and Bioorganic Chemistry, University of Graz, Graz, Austria
- Programa de Estudio y Control de Enfermedades Tropicales (PECET), Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
- Department of Biochemistry, McGill University, Montreal, Canada
| | - Amit Singh Sahrawat
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- Innophore GmbH, Graz, Austria
| | | | - Karl Gruber
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- Innophore GmbH, Graz, Austria
- Field of Excellence BioHealth, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - Tea Pavkov-Keller
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- Field of Excellence BioHealth, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | | | - Alba Guarné
- Department of Biochemistry, McGill University, Montreal, Canada
| | - Sergio Pulido
- Programa de Estudio y Control de Enfermedades Tropicales (PECET), Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
- LifeFactors ZF SAS, Rionegro, Colombia
| | - Marcel Marín-Villa
- Programa de Estudio y Control de Enfermedades Tropicales (PECET), Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Klaus Zangger
- Institute of Chemistry/Organic and Bioorganic Chemistry, University of Graz, Graz, Austria.
- Field of Excellence BioHealth, University of Graz, Graz, Austria.
- BioTechMed-Graz, Graz, Austria.
| | - Nina Gubensäk
- Institute of Molecular Biosciences, University of Graz, Graz, Austria.
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11
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Baltasar-Marchueta M, Llona L, M-Alicante S, Barbolla I, Ibarluzea MG, Ramis R, Salomon AM, Fundora B, Araujo A, Muguruza-Montero A, Nuñez E, Pérez-Olea S, Villanueva C, Leonardo A, Arrasate S, Sotomayor N, Villarroel A, Bergara A, Lete E, González-Díaz H. Identification of Riluzole derivatives as novel calmodulin inhibitors with neuroprotective activity by a joint synthesis, biosensor, and computational guided strategy. Biomed Pharmacother 2024; 174:116602. [PMID: 38636396 DOI: 10.1016/j.biopha.2024.116602] [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: 01/19/2024] [Revised: 04/10/2024] [Accepted: 04/11/2024] [Indexed: 04/20/2024] Open
Abstract
The development of new molecules for the treatment of calmodulin related cardiovascular or neurodegenerative diseases is an interesting goal. In this work, we introduce a novel strategy with four main steps: (1) chemical synthesis of target molecules, (2) Förster Resonance Energy Transfer (FRET) biosensor development and in vitro biological assay of new derivatives, (3) Cheminformatics models development and in vivo activity prediction, and (4) Docking studies. This strategy is illustrated with a case study. Firstly, a series of 4-substituted Riluzole derivatives 1-3 were synthetized through a strategy that involves the construction of the 4-bromoriluzole framework and its further functionalization via palladium catalysis or organolithium chemistry. Next, a FRET biosensor for monitoring Ca2+-dependent CaM-ligands interactions has been developed and used for the in vitro assay of Riluzole derivatives. In particular, the best inhibition (80%) was observed for 4-methoxyphenylriluzole 2b. Besides, we trained and validated a new Networks Invariant, Information Fusion, Perturbation Theory, and Machine Learning (NIFPTML) model for predicting probability profiles of in vivo biological activity parameters in different regions of the brain. Next, we used this model to predict the in vivo activity of the compounds experimentally studied in vitro. Last, docking study conducted on Riluzole and its derivatives has provided valuable insights into their binding conformations with the target protein, involving calmodulin and the SK4 channel. This new combined strategy may be useful to reduce assay costs (animals, materials, time, and human resources) in the drug discovery process of calmodulin inhibitors.
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Affiliation(s)
- Maider Baltasar-Marchueta
- Department of Organic and Inorganic Chemistry, University of the Basque Country UPV/EHU, Leioa 48940, Spain
| | - Leire Llona
- Department of Organic and Inorganic Chemistry, University of the Basque Country UPV/EHU, Leioa 48940, Spain
| | | | - Iratxe Barbolla
- Department of Organic and Inorganic Chemistry, University of the Basque Country UPV/EHU, Leioa 48940, Spain
| | - Markel Garcia Ibarluzea
- Donostia International Physics Center, Donostia, Spain; Departament of Physics, University of the Basque Country, UPV/EHU, Leioa, Spain
| | - Rafael Ramis
- Donostia International Physics Center, Donostia, Spain; Departament of Physics, University of the Basque Country, UPV/EHU, Leioa, Spain
| | - Ane Miren Salomon
- Department of Organic and Inorganic Chemistry, University of the Basque Country UPV/EHU, Leioa 48940, Spain
| | - Brenda Fundora
- Department of Organic and Inorganic Chemistry, University of the Basque Country UPV/EHU, Leioa 48940, Spain
| | - Ariane Araujo
- Biofisika Institute, CSIC-UPV/EHU, Leioa 48940, Spain
| | | | - Eider Nuñez
- Biofisika Institute, CSIC-UPV/EHU, Leioa 48940, Spain
| | - Scarlett Pérez-Olea
- Department of Organic and Inorganic Chemistry, University of the Basque Country UPV/EHU, Leioa 48940, Spain
| | - Christian Villanueva
- Department of Organic and Inorganic Chemistry, University of the Basque Country UPV/EHU, Leioa 48940, Spain
| | - Aritz Leonardo
- Donostia International Physics Center, Donostia, Spain; Departament of Physics, University of the Basque Country, UPV/EHU, Leioa, Spain
| | - Sonia Arrasate
- Department of Organic and Inorganic Chemistry, University of the Basque Country UPV/EHU, Leioa 48940, Spain
| | - Nuria Sotomayor
- Department of Organic and Inorganic Chemistry, University of the Basque Country UPV/EHU, Leioa 48940, Spain
| | | | - Aitor Bergara
- Donostia International Physics Center, Donostia, Spain; Departament of Physics, University of the Basque Country, UPV/EHU, Leioa, Spain.
| | - Esther Lete
- Department of Organic and Inorganic Chemistry, University of the Basque Country UPV/EHU, Leioa 48940, Spain.
| | - Humberto González-Díaz
- Department of Organic and Inorganic Chemistry, University of the Basque Country UPV/EHU, Leioa 48940, Spain; Biofisika Institute, CSIC-UPV/EHU, Leioa 48940, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao 48011, Spain.
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12
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Duc NV, Trang VT, Tuan Anh HL, Vinh LB, Phong NV, Thuan TQ, Hieu NV, Dat NT, Nhan LV, Tuan DT, Tuan Anh L, Thao DT, Tai BH, Cuong NC, Lien LQ, Yang SY. Acetylcholinesterase inhibition studies of alkaloid components from Crinum asiaticum var. sinicum: in vitro assessments by molecular docking and molecular dynamics simulations. JOURNAL OF ASIAN NATURAL PRODUCTS RESEARCH 2024; 26:652-662. [PMID: 37889019 DOI: 10.1080/10286020.2023.2269541] [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: 06/20/2023] [Accepted: 10/07/2023] [Indexed: 10/28/2023]
Abstract
Alkaloids are among the most important and best-known secondary metabolites as sources of new drugs from medicinal plants and marine organisms. A phytochemical investigation of the whole plant of Crinum asiaticum var. sinicum resulted in the isolation of seven alkaloids (1-7), including one new dimeric compound, bis-(-)-8-demethylmaritidine (1). Their structures were elucidated using NMR and HR-ESI-MS. The absolute configuration of new compound 1 was established by circular dichroism spectroscopy. All isolated compounds were evaluated for their inhibitory effects on acetylcholinesterase (AChE) activity in vitro. Among them, compound 1 exhibited the most potent AChE inhibition. Moreover, molecular docking and molecular dynamics simulations were carried out for the most active compound to investigate their binding interactions and dynamics behavior of the AChE protein-ligand complex. Therefore, compound 1 may be a potential candidate for effectively treating Alzheimer's disease.
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Affiliation(s)
- Ngo Viet Duc
- Center for Research and Technology Transfer (CRTT), Vietnam Academy of Science and Technology (VAST), Hanoi 10072, Vietnam
| | - Vu Thi Trang
- Center for Research and Technology Transfer (CRTT), Vietnam Academy of Science and Technology (VAST), Hanoi 10072, Vietnam
- Graduate University of Science and Technology, VAST, Hanoi 10072, Vietnam
| | - Hoang Le Tuan Anh
- Center for Research and Technology Transfer (CRTT), Vietnam Academy of Science and Technology (VAST), Hanoi 10072, Vietnam
- Graduate University of Science and Technology, VAST, Hanoi 10072, Vietnam
| | - Le Ba Vinh
- Institute of Marine Biochemistry, VAST, Hanoi 10072, Vietnam
- Faculty of Chemical Technology, Hanoi University of Industry, Hanoi 11900, Vietnam
| | | | - Tran Quang Thuan
- Center for Research and Technology Transfer (CRTT), Vietnam Academy of Science and Technology (VAST), Hanoi 10072, Vietnam
| | - Ngo Van Hieu
- Center for Research and Technology Transfer (CRTT), Vietnam Academy of Science and Technology (VAST), Hanoi 10072, Vietnam
| | - Nguyen Tien Dat
- Center for Research and Technology Transfer (CRTT), Vietnam Academy of Science and Technology (VAST), Hanoi 10072, Vietnam
| | - Le Van Nhan
- Center for Research and Technology Transfer (CRTT), Vietnam Academy of Science and Technology (VAST), Hanoi 10072, Vietnam
| | - Do Thanh Tuan
- ThaiBinh University of Medicine and Pharmacy, Thai Binh 06100, Vietnam
| | - Le Tuan Anh
- Mientrung Institute for Scientific Research, VNMN, VAST, Hanoi 10072, Vietnam
| | - Do Thi Thao
- Institute of Biotechnology, VAST, Hanoi 10072, Vietnam
| | - Bui Huu Tai
- Institute of Marine Biochemistry, VAST, Hanoi 10072, Vietnam
| | - Nguyen Cao Cuong
- Department of Medicine and Pharmacy, Yersin University, Da Lat 66100, Vietnam
| | - Le Quynh Lien
- Institute of Marine Biochemistry, VAST, Hanoi 10072, Vietnam
| | - Seo Young Yang
- Department of Biology Education, Teachers College and Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu 41566, Republic of Korea
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13
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Pratiwi E, Raya I, Natsir H, Irfandi R, Taba P, Arfah R, Rasyid H, Hala Y, Kasim S, Khaerunnisa AB, Ilham B, Mazaya M, Tanzil Y, Luthfiana D. Investigations of Ni(II)Cysteine-Tyrosine Dithiocarbamate Complex: Synthesis, Characterization, Molecular Docking, Molecular Dynamic, and Anticancer Activity on MCF-7 Breast Cancer Cell Line. Asian Pac J Cancer Prev 2024; 25:1301-1313. [PMID: 38679991 PMCID: PMC11162741 DOI: 10.31557/apjcp.2024.25.4.1301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 04/10/2024] [Indexed: 05/01/2024] Open
Abstract
OBJECTIVE Breast cancer ranks second in terms of the highest number of cancer deaths for women worldwide and is one of the leading causes of death from cancer in women. The drug that is often used for chemotherapy is cisplatin. However, cisplatin drugs have a number of problems, including lack of selectivity, unwanted side effects, resistance, and toxicity in the body. In this work, we investigated Ni(II) cysteine-tyrosine dithiocarbamate complex against breast cancer. METHODS Research on the new complex compound Ni(II) cysteine-tyrosine dithiocarbamate have several stages including synthesis, characterization, in-silico and in-vitro testing of MCF-7 cells for anticancer drugs. The synthesis involved reacting cysteine, CS2, KOH and tyrosine with Mn metal. The new complex compound Ni(II) cysteine-tyrosine dithiocarbamate has been synthesized, characterized, and tested in vitro MCF-7 cells for anticancer drugs. Characterization tests such as melting point, conductivity, SEM-EDS, UV Vis, XRD, and FT-IR spectroscopy have been carried out. RESULT The synthesis yielded a 60,16%, conversion with a melting point of 216-218 oC and a conductivity value of 0.4 mS/cm. In vitro test results showed morphological changes (apoptosis) in MCF-7 cancer cells starting at a sample concentration of 250 µg/mL and an IC50 value of 618.40 µg/mL. Molecular docking study of Ni(II) cysteine-tyrosine dithiocarbamate complex identified with 4,4',4''-[(2R)-butane-1,1,2-triyl]triphenol - Estrogen α showing active site with acidic residue amino E323, M388, L387, G390 and I389. Hydrophobic and hydrophobic bonds are seen in Ni(II) cysteine-tyrosine dithiocarbamate - Estrogen α has a binding energy of -80.9429 kJ /mol. CONCLUSION there were 5 residues responsible for maintaining the ligand binding stable. The compound had significant Hbond contact intensity, however, it was not strong enough to make a significant anticancer effect. Though the synthesized compound shows low bioactivity, this research is expected to give valuable insight into the effect of molecular structure on anticancer activity.
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Affiliation(s)
- Eka Pratiwi
- Department of Chemistry, Faculty of Mathematics and Natural Science, Hasanuddin University, Makassar 90245, Indonesia.
| | - Indah Raya
- Department of Chemistry, Faculty of Mathematics and Natural Science, Hasanuddin University, Makassar 90245, Indonesia.
| | - Hasnah Natsir
- Department of Chemistry, Faculty of Mathematics and Natural Science, Hasanuddin University, Makassar 90245, Indonesia.
| | - Rizal Irfandi
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Negeri Makassar, Makassar, Jalan Daeng Tata Raya Makassar, 90244, Indonesia.
| | - Paulina Taba
- Department of Chemistry, Faculty of Mathematics and Natural Science, Hasanuddin University, Makassar 90245, Indonesia.
| | - Rugaiyah Arfah
- Department of Chemistry, Faculty of Mathematics and Natural Science, Hasanuddin University, Makassar 90245, Indonesia.
| | - Herlina Rasyid
- Department of Chemistry, Faculty of Mathematics and Natural Science, Hasanuddin University, Makassar 90245, Indonesia.
| | - Yusafir Hala
- Department of Chemistry, Faculty of Mathematics and Natural Science, Hasanuddin University, Makassar 90245, Indonesia.
| | - Syahruddin Kasim
- Department of Chemistry, Faculty of Mathematics and Natural Science, Hasanuddin University, Makassar 90245, Indonesia.
| | - Andi Besse Khaerunnisa
- Department of Chemistry, Faculty of Mathematics and Natural Science, Hasanuddin University, Makassar 90245, Indonesia.
| | - Baso Ilham
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga, Komplek Kampus C UNAIR, Jl. Mulyorejo-60115, Surabaya, Indonesia.
| | - Maulida Mazaya
- Research Center for Computing, Research Organization for Electronics and Informatics, National Research and Innovation Agency (BRIN), Cibinong Science Center, Jl. Raya Jakarta-Bogor KM 46, Cibinong 16911, West Java, Indonesia.
| | - Yosua Tanzil
- Department of Chemistry, Faculty of Mathematics and Natural Science, Gadjah Mada University, Yogyakarta 55281, Indonesia.
| | - Dewi Luthfiana
- Master Pogram, Graduate School of Bioagricultural Sciences, Department of Applied Biosciences, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8601, Japan.
- Bioinformatics Research Center, Indonesian Institute of Bioinformatics (INBIO), Malang 65162, Indonesia.
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14
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Gholami A, Minai-Tehrani D, Farewell A, Eriksson LA. Discovery of novel inhibitors for Pseudomonas aeruginosa lipase enzyme from in silico and in vitro studies. J Biomol Struct Dyn 2024; 42:2197-2210. [PMID: 37098781 DOI: 10.1080/07391102.2023.2203258] [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: 12/28/2022] [Accepted: 04/10/2023] [Indexed: 04/27/2023]
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen prone to developing drug-resistance and is a major cause of infection for burn patients and patients suffering from cystic fibrosis or are hospitalized in intensive care units. One of the virulence factors of this bacterium is the lipase enzyme that degrades the extracellular matrix of the host tissue and promotes invasion. Bromhexine is a mucolytic drug and has recently been reported to function as a competitive inhibitor of lipase with an IC50 value of 49 µM. In the present study, an attempt was made to identify stronger inhibitors from the ChEMBL database of bioactive compounds, as compared to the reference compound Bromhexine. Following docking and MD simulations, four hit compounds (N1-N4) were selected that showed promising binding modes and low RMSD values indicative of stable protein-ligand complexes. From subsequent binding pose metadynamics (BPMD) simulations, two of these (N2 and N4) stood out as more potent than Bromhexine, displaying stable interactions with residues in the catalytic site of the enzyme. Biological investigations were performed for all four compounds. Among them, the same two hit compounds were found to be the most effective binders with IC50 values of 22.1 and 27.5 µM, respectively; i.e. roughly twice as efficient as the reference Bromhexine. Taken together, our results show that these hits can be promising new candidates to use as leads for the development of drugs targeting the P. aeruginosa lipase enzyme.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Asma Gholami
- Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
- Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden
| | - Dariush Minai-Tehrani
- Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Anne Farewell
- Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden
- Centre for Antibiotic Resistance Research, University of Gothenburg, Göteborg, Sweden
| | - Leif A Eriksson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden
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15
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Baselious F, Hilscher S, Robaa D, Barinka C, Schutkowski M, Sippl W. Comparative Structure-Based Virtual Screening Utilizing Optimized AlphaFold Model Identifies Selective HDAC11 Inhibitor. Int J Mol Sci 2024; 25:1358. [PMID: 38279359 PMCID: PMC10816272 DOI: 10.3390/ijms25021358] [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: 12/11/2023] [Revised: 01/14/2024] [Accepted: 01/20/2024] [Indexed: 01/28/2024] Open
Abstract
HDAC11 is a class IV histone deacylase with no crystal structure reported so far. The catalytic domain of HDAC11 shares low sequence identity with other HDAC isoforms, which makes conventional homology modeling less reliable. AlphaFold is a machine learning approach that can predict the 3D structure of proteins with high accuracy even in absence of similar structures. However, the fact that AlphaFold models are predicted in the absence of small molecules and ions/cofactors complicates their utilization for drug design. Previously, we optimized an HDAC11 AlphaFold model by adding the catalytic zinc ion and minimization in the presence of reported HDAC11 inhibitors. In the current study, we implement a comparative structure-based virtual screening approach utilizing the previously optimized HDAC11 AlphaFold model to identify novel and selective HDAC11 inhibitors. The stepwise virtual screening approach was successful in identifying a hit that was subsequently tested using an in vitro enzymatic assay. The hit compound showed an IC50 value of 3.5 µM for HDAC11 and could selectively inhibit HDAC11 over other HDAC subtypes at 10 µM concentration. In addition, we carried out molecular dynamics simulations to further confirm the binding hypothesis obtained by the docking study. These results reinforce the previously presented AlphaFold optimization approach and confirm the applicability of AlphaFold models in the search for novel inhibitors for drug discovery.
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Affiliation(s)
- Fady Baselious
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, 06120 Halle (Saale), Germany; (F.B.); (S.H.); (D.R.)
| | - Sebastian Hilscher
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, 06120 Halle (Saale), Germany; (F.B.); (S.H.); (D.R.)
| | - Dina Robaa
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, 06120 Halle (Saale), Germany; (F.B.); (S.H.); (D.R.)
| | - Cyril Barinka
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, 252 50 Vestec, Czech Republic;
| | - Mike Schutkowski
- Charles Tanford Protein Center, Department of Enzymology, Institute of Biochemistry and Biotechnology, Martin-Luther-University of Halle-Wittenberg, 06120 Halle (Saale), Germany;
| | - Wolfgang Sippl
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, 06120 Halle (Saale), Germany; (F.B.); (S.H.); (D.R.)
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16
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Alghamdi MA, Azam F, Alam P. Deciphering Campylobacter jejuni DsbA1 protein dynamics in the presence of anti-virulent compounds: a multi-pronged computer-aided approach. J Biomol Struct Dyn 2024:1-17. [PMID: 38230450 DOI: 10.1080/07391102.2024.2302945] [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: 08/23/2023] [Accepted: 01/02/2024] [Indexed: 01/18/2024]
Abstract
The current study aims to evaluate Asinex library compounds against Campylobacter jejuni DsbA1 protein, a thiol disulfide oxidoreductase enzyme that plays a major role in the oxidative folding of bacterial virulence proteins, making it a promising anti-viral drug target. By employing several techniques of computer-aided drug design, BDC25697459, BDD33601083, and BDC30129064 were identified with binding energy scores of -8.8 kcal/mol, -8.8 kcal/mol, and -8.3 kcal/mol, respectively. However, the control molecule, tetraethylene glycol, exhibited a binding energy score of -7.0 kcal/mol. The control, BDD33601083, and BDC30129064 were unveiled to bind the same co-crystallized binding site (pocket 1), while BDC25697459 interacted with a new binding pocket (pocket 2) adjacent to the control binding region. The molecular dynamics simulation showed that complexes exhibit stable dynamics without significant global or residue-level fluctuations. The average RMSD values were in the range of 2.07 Å-2.45 Å. Similarly, mean RMSF was recorded between 1.30 and 1.42 Å. The C. jejuni DsbA1 was also observed as compact in the presence of the compounds, showing a mean RoG value in the range of 16.42 Å-16.55 Å. In terms of MM/PBSA binding energy, the BDC30129064 complex was ranked top with -44.88 ± 4.14 kcal/mol, whereas the positive control molecule exhibited -22.22 ± 3.33 kcal/mol. From a pharmacokinetic perspective, the compounds are suitable candidates for clinical trial investigation. Preliminary computational analysis of these virtual hits indicates that these compounds have a low potential for ADME and toxicity-associated liabilities. In summary, the compounds displayed a high affinity for the C. jejuni DsbA1 protein, indicating potential efficacy that requires further investigation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mashael A Alghamdi
- Department of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Faizul Azam
- Department of Pharmaceutical Chemistry and Pharmacognosy, Unaizah College of Pharmacy, Qassim University, Buraydah, Saudi Arabia
| | - Prawez Alam
- Department of Pharmacognosy, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al Kharj, Saudi Arabia
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17
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Tettevi EJ, Kuevi DNO, Sumabe BK, Simpong DL, Maina MB, Dongdem JT, Osei-Atweneboana MY, Ocloo A. In Silico Identification of a Potential TNF-Alpha Binder Using a Structural Similarity: A Potential Drug Repurposing Approach to the Management of Alzheimer's Disease. BIOMED RESEARCH INTERNATIONAL 2024; 2024:9985719. [PMID: 38221912 PMCID: PMC10787656 DOI: 10.1155/2024/9985719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 11/25/2023] [Accepted: 12/13/2023] [Indexed: 01/16/2024]
Abstract
Introduction Alzheimer's disease (AD) is a neurodegenerative disorder with no conclusive remedy. Yohimbine, found in Rauwolfia vomitoria, may reduce brain inflammation by targeting tumour necrosis factor-alpha (TNFα), implicated in AD pathogenesis. Metoserpate, a synthetic compound, may inhibit TNFα. The study is aimed at assessing the potential utility of repurposing metoserpate for TNFα inhibition to reduce neuronal damage and inflammation in AD. The development of safe and effective treatments for AD is crucial to address the growing burden of the disease, which is projected to double over the next two decades. Methods Our study repurposed an FDA-approved drug as TNFα inhibitor for AD management using structural similarity studies, molecular docking, and molecular dynamics simulations. Yohimbine was used as a reference compound. Molecular docking used SeeSAR, and molecular dynamics simulation used GROMACS. Results Metoserpate was selected from 10 compounds similar to yohimbine based on pharmacokinetic properties and FDA approval status. Molecular docking and simulation studies showed a stable interaction between metoserpate and TNFα over 100 ns (100000 ps). This suggests a reliable and robust interaction between the protein and ligand, supporting the potential utility of repurposing metoserpate for TNFα inhibition in AD treatment. Conclusion Our study has identified metoserpate, a previously FDA-approved antihypertensive agent, as a promising candidate for inhibiting TNFα in the management of AD.
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Affiliation(s)
- Edward Jenner Tettevi
- Department of Biochemistry, Cell and Molecular Biology, School of Biological Science, University of Ghana, Legon, Accra, P.O. Box LG 25, Ghana
- West African Centre for Cell Biology of Infectious Pathogens, School of Biological Science, University of Ghana, Legon, Accra, P.O. Box LG 25, Ghana
- Biomedical and Public Health Research Unit, Council for Scientific and Industrial Research-Water Research Institute, Accra, P.O. Box M 32, Ghana
| | - Deryl Nii Okantey Kuevi
- Biomedical and Public Health Research Unit, Council for Scientific and Industrial Research-Water Research Institute, Accra, P.O. Box M 32, Ghana
| | - Balagra Kasim Sumabe
- Biomedical and Public Health Research Unit, Council for Scientific and Industrial Research-Water Research Institute, Accra, P.O. Box M 32, Ghana
| | - David Larbi Simpong
- Department of Medical Laboratory Sciences, College of Health and Allied Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Mahmoud B. Maina
- Serpell Laboratory, Sussex Neuroscience, School of Life Sciences, University of Sussex, UK
- Biomedical Science Research and Training Centre, College of Medical Sciences, Yobe State University, Damaturu, Nigeria
| | - Julius T. Dongdem
- Department of Biochemistry and Molecular Medicine, School of Medicine, University for Development Studies, Tamale Campus, Ghana
| | - Mike Y. Osei-Atweneboana
- Biomedical and Public Health Research Unit, Council for Scientific and Industrial Research-Water Research Institute, Accra, P.O. Box M 32, Ghana
- CSIR-College of Science and Technology, 2nd CSIR Close, Airport Residential Area, Behind Golden Tulip Hotel, Greater Accra Region, Ghana
| | - Augustine Ocloo
- Department of Biochemistry, Cell and Molecular Biology, School of Biological Science, University of Ghana, Legon, Accra, P.O. Box LG 25, Ghana
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18
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Mahdizadeh SJ, Grandén J, Pelizzari-Raymundo D, Guillory X, Carlesso A, Chevet E, Eriksson LA. Different binding modalities of quercetin to inositol-requiring enzyme 1 of S. cerevisiae and human lead to opposite regulation. Commun Chem 2024; 7:6. [PMID: 38177336 PMCID: PMC10767055 DOI: 10.1038/s42004-023-01092-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 12/20/2023] [Indexed: 01/06/2024] Open
Abstract
The flavonoid Quercetin (Qe) was identified as an activator of Inositol-requiring enzyme 1 (IRE1) in S. cerevisiae (scIre1p), but its impact on human IRE1 (hIRE1) remains controversial due to the absence of a conserved Qe binding site. We have explored the binding modes and effect of Qe on both scIre1p and hIRE1 dimers using in silico and in vitro approaches. The activation site in scIre1p stably accommodates both Qe and its derivative Quercitrin (Qi), thus enhancing the stability of the RNase pocket. However, the corresponding region in hIRE1 does not bind any of the two molecules. Instead, we show that both Qe and Qi block the RNase activity of hIRE1 in vitro, with sub-micromolar IC50 values. Our results provide a rationale for why Qe is an activator in scIre1p but a potent inhibitor in hIRE1. The identification of a new allosteric site in hIRE1 opens a promising window for drug development and UPR modulation.
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Affiliation(s)
- S Jalil Mahdizadeh
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30, Göteborg, Sweden
| | - Johan Grandén
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30, Göteborg, Sweden
| | - Diana Pelizzari-Raymundo
- INSERM U1242, Université de Rennes, Rennes, France
- Centre de Lutte contre le Cancer Eugène Marquis, Rennes, France
| | - Xavier Guillory
- INSERM U1242, Université de Rennes, Rennes, France
- Centre de Lutte contre le Cancer Eugène Marquis, Rennes, France
- Univ Rennes, CNRS, ISCR - UMR 6226, F-35000, Rennes, France
| | - Antonio Carlesso
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30, Göteborg, Sweden
- Department of Pharmacology, Sahlgrenska Academy, University of Gothenburg, SE-405 31, Gothenburg, Sweden
| | - Eric Chevet
- INSERM U1242, Université de Rennes, Rennes, France.
- Centre de Lutte contre le Cancer Eugène Marquis, Rennes, France.
| | - Leif A Eriksson
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30, Göteborg, Sweden.
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19
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Ledneczki I, Némethy Z, Molnár KD, Tapolcsányi P, Ilkei V, Vágó I, Kolok S, Thán M, Laszy J, Balázs O, Krámos B, Szigetvári Á, Bata I, Makó A, Visegrády A, Fodor L, Vastag M, Lévay G, Lendvai B, Greiner I, Éles J. Optimization of Novel α7 Nicotinic Acetylcholine Receptor Positive Allosteric Modulators and the Discovery of a Preclinical Development Candidate Molecule (RGH-560). J Med Chem 2023; 66:16276-16302. [PMID: 37989278 DOI: 10.1021/acs.jmedchem.3c01635] [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: 11/23/2023]
Abstract
During optimization of a previously identified lead compound, attempts were made to optimize the reactive indole structural element, the suboptimal metabolic stability, as well as the low kinetic solubility. It was concluded that the indole was important for in vitro activity. With the aim of further improvements, more thorough modifications were also carried out. As a result, a new chemotype (the azetidinespirochromone family) was identified, which proved to be 1 order of magnitude less lipophilic retaining the same high level of in vitro potency as the lead series itself, however, with improved metabolic stability and kinetic solubility. Compound 53 showed the most balanced physicochemical and pharmacological profile with significant in vivo efficacy in the scopolamine-induced amnesia test. Based on these promising results, cognitive enhancement through the positive modulation of α7 nAChRs appears to be a viable approach. Compound 53 was selected to be a preclinical development candidate (as RGH-560).
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Affiliation(s)
| | - Zsolt Némethy
- Gedeon Richter Plc, 19-21 Gyömői útca, Budapest H-1103, Hungary
| | | | - Pál Tapolcsányi
- Gedeon Richter Plc, 19-21 Gyömői útca, Budapest H-1103, Hungary
| | - Viktor Ilkei
- Gedeon Richter Plc, 19-21 Gyömői útca, Budapest H-1103, Hungary
| | - István Vágó
- Gedeon Richter Plc, 19-21 Gyömői útca, Budapest H-1103, Hungary
| | - Sándor Kolok
- Gedeon Richter Plc, 19-21 Gyömői útca, Budapest H-1103, Hungary
| | - Márta Thán
- Gedeon Richter Plc, 19-21 Gyömői útca, Budapest H-1103, Hungary
| | - Judit Laszy
- Gedeon Richter Plc, 19-21 Gyömői útca, Budapest H-1103, Hungary
| | - Ottilia Balázs
- Gedeon Richter Plc, 19-21 Gyömői útca, Budapest H-1103, Hungary
| | - Balázs Krámos
- Gedeon Richter Plc, 19-21 Gyömői útca, Budapest H-1103, Hungary
| | - Áron Szigetvári
- Gedeon Richter Plc, 19-21 Gyömői útca, Budapest H-1103, Hungary
| | - Imre Bata
- Gedeon Richter Plc, 19-21 Gyömői útca, Budapest H-1103, Hungary
| | - Attila Makó
- Gedeon Richter Plc, 19-21 Gyömői útca, Budapest H-1103, Hungary
| | | | - László Fodor
- Gedeon Richter Plc, 19-21 Gyömői útca, Budapest H-1103, Hungary
| | - Mónika Vastag
- Gedeon Richter Plc, 19-21 Gyömői útca, Budapest H-1103, Hungary
| | - György Lévay
- Gedeon Richter Plc, 19-21 Gyömői útca, Budapest H-1103, Hungary
| | - Balázs Lendvai
- Gedeon Richter Plc, 19-21 Gyömői útca, Budapest H-1103, Hungary
| | - István Greiner
- Gedeon Richter Plc, 19-21 Gyömői útca, Budapest H-1103, Hungary
| | - János Éles
- Gedeon Richter Plc, 19-21 Gyömői útca, Budapest H-1103, Hungary
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20
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Mittal L, Tonk RK, Awasthi A, Asthana S. Harnessing the druggability at orthosteric and allosteric sites of PD-1 for small molecule discovery by an integrated in silico pipeline. Comput Biol Chem 2023; 107:107965. [PMID: 37826990 DOI: 10.1016/j.compbiolchem.2023.107965] [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: 06/08/2023] [Revised: 09/06/2023] [Accepted: 09/25/2023] [Indexed: 10/14/2023]
Abstract
The PD-1/PD-L1 interaction is a promising target for small molecule inhibitors in cancer immunotherapy, but targeting this interface has been challenging. While efforts have been made to identify compounds that target the orthosteric sites, no reports have explored the potential of small molecules to target the allosteric region of PD-1. Therefore, our study aims to establish a pipeline to identify small molecules that can effectively bind to either the orthosteric or allosteric pockets of PD-1. We categorized the PD-1 interface into two hot-spot zones (P-and N-zones) based on extensive analysis of its structural, dynamical, and energetic properties. These zones correspond to the orthosteric and allosteric PPI sites, respectively, targeted by monoclonal antibodies. We used a guided virtual screening workflow to identify hits from ∼7 million compounds library, which were then clustered based on structural similarity and assessed by interaction fingerprinting. The selective and diverse chemical representatives were subjected to MD simulations and binding energetics calculations to filter out false positives and identify actual binders. Binding poses metadynamics calculations confirmed the stability of the final hits in the pocket. This study emphasizes the need for an integrated pipeline that uses molecular dynamics simulations and binding energetics to identify potential binders for the dynamic PD-1/PD-L1 interface, due to the lack of small molecule co-crystals. Only a few potential binders were discovered from a large pool of molecules targeting both the allosteric and orthosteric zones. Our results suggest that the allosteric site has more potential than the orthosteric site for inhibitor design. The identified "computational hits" hold potential as starting points for in vitro evaluations followed by hit-to-lead optimization. Overall, this study represents an effort to establish a computational pipeline for exploring and enriching both the allosteric and orthosteric sites of PPI interfaces, "a tough but indispensable nut to crack".
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Affiliation(s)
- Lovika Mittal
- Computational Biophysics and CADD group, Computational and Mathematical Biology Center (CMBC), Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana, India; Delhi Pharmaceutical Science Research University (DPSRU), New Delhi, India
| | - Rajiv K Tonk
- Delhi Pharmaceutical Science Research University (DPSRU), New Delhi, India
| | - Amit Awasthi
- Computational Biophysics and CADD group, Computational and Mathematical Biology Center (CMBC), Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana, India
| | - Shailendra Asthana
- Computational Biophysics and CADD group, Computational and Mathematical Biology Center (CMBC), Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana, India.
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21
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Balogun FO, Singh K, Rampadarath A, Akoonjee A, Naidoo K, Sabiu S. Cheminformatics identification of modulators of key carbohydrate-metabolizing enzymes from C. cujete for type-2 diabetes mellitus intervention. J Diabetes Metab Disord 2023; 22:1299-1317. [PMID: 37969920 PMCID: PMC10638353 DOI: 10.1007/s40200-023-01249-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 06/07/2023] [Indexed: 11/17/2023]
Abstract
Purpose The therapeutic use of oral hypoglycaemic agents in the management of type-2 diabetes mellitus (T2DM) is without adverse effects; thus, calls for alternative and novel candidates from natural products in medicinal plants. Method The study explored molecular docking and molecular dynamics (MD) simulation approaches to identify key antidiabetic metabolites from Crescentia cujete. Results Molecular docking results identified four and/or five best compounds against each target enzyme (alpha-glucosidase, dipeptidyl peptidase-IV, aldose reductase, and protein tyrosine phosphatase-1B (PTP-1B)) implicated in diabetes. The resulting complexes (except against PTP-1B) had higher docking scores above respective standards (acarbose, Diprotin A, ranirestat). The MD simulation results revealed compounds such as benzoic acid (-48.414 kcal/mol) and phytol (-45.112 kcal/mol) as well as chlorogenic acid (-42.978 kcal/mol) and naringenin (-31.292 kcal/mol) had higher binding affinities than the standards [acarbose (-28.248 kcal/mol), ranirestat (-21.042 kcal/mol)] against alpha-glucosidase and aldose reductase, respectively while Diprotin A (-45.112 kcal/mol) and ursolic acid (-18.740 kcal/mol) presented superior binding affinities than the compounds [luteolin (-41.957 kcal/mol and naringenin (-16.518 kcal/mol)] against DPP-IV and PTP-1B respectively. Conclusion While isoflavone (alpha-glucosidase), xylocaine (DPP-IV), luteolin (aldose reductase,) and chlorogenic acid (PTP-1B) were affirmed as the best inhibitors of respective enzyme targets, luteolin, and chlorogenic acid may be suggested and proposed as probable candidates against T2DM and related retinopathy complication based on their structural stability, compactness and affinity for three (DPP-IV, aldose reductase, and PTP-1B) of the four targets investigated. Further studies are warranted in vitro and in vivo on the antihyperglycaemic effects of these drug candidates. Supplementary Information The online version contains supplementary material available at 10.1007/s40200-023-01249-7.
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Affiliation(s)
- Fatai Oladunni Balogun
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, P.O. Box 1334, Durban, 4000 South Africa
| | - Karishma Singh
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, P.O. Box 1334, Durban, 4000 South Africa
- Department of Nature Conservation, Mangosuthu University of Technology, Mangosuthu, South Africa
| | - Athika Rampadarath
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, P.O. Box 1334, Durban, 4000 South Africa
| | - Ayesha Akoonjee
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, P.O. Box 1334, Durban, 4000 South Africa
| | - Kayleen Naidoo
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, P.O. Box 1334, Durban, 4000 South Africa
| | - Saheed Sabiu
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, P.O. Box 1334, Durban, 4000 South Africa
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22
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Saar A, Ghahremanpour MM, Tirado-Rives J, Jorgensen WL. Assessing Metadynamics and Docking for Absolute Binding Free Energy Calculations Using Severe Acute Respiratory Syndrome Coronavirus 2 Main Protease Inhibitors. J Chem Inf Model 2023; 63:7210-7218. [PMID: 37934762 DOI: 10.1021/acs.jcim.3c01453] [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: 11/09/2023]
Abstract
Absolute binding free energy (ABFE) calculations can be an important part of the drug discovery process by identifying molecules that have the potential to be strong binders for a biomolecular target. Recent work has used free energy perturbation (FEP) theory for these calculations, focusing on a set of 16 inhibitors of the severe acute respiratory syndrome coronavirus 2 main protease (Mpro). Herein, the same data set is evaluated by metadynamics (MetaD), four different docking programs, and molecular mechanics with generalized Born and surface area solvation. MetaD yields a Kendall τ distance of 0.28 and Pearson r2 of 0.49, which reflect somewhat less accuracy than that from the ABFE FEP results. Notably, it is demonstrated that an ensemble docking protocol by which each ligand is docked into the 13 crystal structures in this data set provides improved performance, particularly when docking is carried out with Glide XP (Kendall τ distance = 0.20, Pearson r2 = 0.71), Glide SP (Kendall τ distance = 0.19, Pearson r2 = 0.66), or AutoDock 4 (Kendall τ distance = 0.21, Pearson r2 = 0.55). The best results are obtained with "superconsensus" docking by averaging the 52 results for each compound using the 4 docking protocols and all 13 crystal structures (Kendall τ distance = 0.18, Pearson r2 = 0.73).
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Affiliation(s)
- Anastasia Saar
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | | | - Julian Tirado-Rives
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - William L Jorgensen
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
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23
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Tian Y, Zhang M, Heng P, Hou H, Wang B. Computational Investigations on Reaction Mechanisms of the Covalent Inhibitors Ponatinib and Analogs Targeting the Extracellular Signal-Regulated Kinases. Int J Mol Sci 2023; 24:15223. [PMID: 37894903 PMCID: PMC10607051 DOI: 10.3390/ijms242015223] [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: 09/16/2023] [Revised: 10/08/2023] [Accepted: 10/14/2023] [Indexed: 10/29/2023] Open
Abstract
As an important cancer therapeutic target, extracellular signal-regulated kinases (ERK) are involved in triggering various cellular responses in tumors. Regulation of the ERK signaling pathway by the small molecular inhibitors is highly desired for the sake of cancer therapy. In contrast to the routine inhibitors targeting ERKs through long-range non-bonding interactions, Ponatinib, a covalent inhibitor to ERK2 with a macrocyclic structure characterized by the α,β-C=C unsaturated ketone, can form the stable -C(S)-C(H)-type complex via the four-center barrier due to the nucleophilic addition reaction of the thiol group of the Cys166 residue of ERK2 with the C=C double bond of Ponatinib with reaction free-energy barrier of 47.2 kcal/mol. Reaction mechanisms for the covalent binding were calculated using QM/MM methods and molecular dynamics simulations. The interaction modes and the corresponding binding free energies were obtained for the non-covalent and covalent complexation. The binding free energies of the non-covalent and covalent inhibitions are 14.8 kcal/mol and 33.4 kcal/mol, respectively. The mechanistic study stimulated a rational design on the modified Ponatinib structure by substituting the C=C bond with the C=N bond. It was demonstrated that the new compound exhibits better inhibition activity toward ERK2 in term of both thermodynamic and kinetic aspects through the covalent binding with a lower reaction free-energy barrier of 23.1 kcal/mol. The present theoretical work sheds new light on the development of the covalent inhibitors for the regulation of ERKs.
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Affiliation(s)
| | | | | | | | - Baoshan Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China; (Y.T.); (M.Z.); (P.H.); (H.H.)
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24
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Das AP, Nandekar P, Mathur P, Agarwal SM. A systematic pipeline of protein structure selection for computer-aided drug discovery: A case study on T790M/L858R mutant EGFR structures. Protein Sci 2023; 32:e4740. [PMID: 37515373 PMCID: PMC10443354 DOI: 10.1002/pro.4740] [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: 02/22/2023] [Revised: 07/24/2023] [Accepted: 07/26/2023] [Indexed: 07/30/2023]
Abstract
Virtual screening (VS) is a routine method to evaluate chemical libraries for lead identification. Therefore, the selection of appropriate protein structures for VS is an essential prerequisite to identify true actives during docking. But the presence of several crystal structures of the same protein makes it difficult to select one or few structures rationally for screening. Therefore, a computational prioritization protocol has been developed for shortlisting crystal structures that identify true active molecules with better efficiency. As identification of small-molecule inhibitors is an important clinical requirement for the T790M/L858R (TMLR) EGFR mutant, it has been selected as a case study. The approach involves cross-docking of 21 co-crystal ligands with all the structures of the same protein to select structures that dock non-native ligands with lower RMSD. The cross docking performance was then correlated with ligand similarity and binding-site conformational similarity. Eventually, structures were shortlisted by integrating cross-docking performance, and ligand and binding-site similarity. Thereafter, binding pose metadynamics was employed to identify structures having stable co-crystal ligands in their respective binding pockets. Finally, different enrichment metrics like BEDROC, RIE, AUAC, and EF1% were evaluated leading to the identification of five TMLR structures (5HCX, 5CAN, 5CAP, 5CAS, and 5CAO). These structures docked a number of non-native ligands with low RMSD, contain structurally dissimilar ligands, have conformationally dissimilar binding sites, harbor stable co-crystal ligands, and also identify true actives early. The present approach can be implemented for shortlisting protein targets of any other important therapeutic kinases.
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Affiliation(s)
- Agneesh Pratim Das
- Bioinformatics Division, ICMR—National Institute of Cancer Prevention and ResearchNoidaUttar PradeshIndia
- Amity Institute of BiotechnologyAmity University Uttar PradeshNoidaUttar PradeshIndia
| | | | - Puniti Mathur
- Amity Institute of BiotechnologyAmity University Uttar PradeshNoidaUttar PradeshIndia
| | - Subhash M. Agarwal
- Bioinformatics Division, ICMR—National Institute of Cancer Prevention and ResearchNoidaUttar PradeshIndia
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25
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Iksen I, Seephan S, Limprasutr V, Sinsook S, Buaban K, Chamni S, Pongrakhananon V. Preclinical Characterization of 22-(4'-Pyridinecarbonyl) Jorunnamycin A against Lung Cancer Cell Invasion and Angiogenesis via AKT/mTOR Signaling. ACS Pharmacol Transl Sci 2023; 6:1143-1154. [PMID: 37588759 PMCID: PMC10425992 DOI: 10.1021/acsptsci.3c00046] [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: 03/07/2023] [Indexed: 08/18/2023]
Abstract
Non-small-cell lung cancer (NSCLC), the most prevalent form of lung cancer, is associated with an unfavorable prognosis owing to its high rate of metastasis. Thus, the identification of new drugs with potent anticancer activities is essential to improve the clinical outcome of this disease. Marine organisms exhibit a diverse source of biologically active compounds with anticancer effects. The anticancer effects of jorunnamycin A (JA) derived from the Thai blue sponge (Xestospongia sp.) and 22-(4'-pyridinecarbonyl) jorunnamycin A (22-(4'-py)-JA), the semisynthetic derivative of JA, have been reported. The present study aimed to investigate the impact of 22-(4'-py)-JA on NSCLC metastasis using in vitro, in vivo, and in silico approaches. The JA derivative inhibited tumor cell invasion and tube formation in human umbilical vein endothelial cells (HUVECs). The computational analysis demonstrated strong and stable interactions between 22-(4'-py)-JA and the AKT protein. Further examinations into the molecular mechanisms revealed the suppression of AKT/mTOR/p70S6K signaling by 22-(4'-py)-JA, leading to the downregulation of matrix metalloproteinases (MMP-2 and MMP-9), hypoxia-inducible factor-1α (HIF-1α), and vascular endothelial growth factor (VEGF). Furthermore, 22-(4'-py)-JA suppressed in vivo metastasis by decreasing the number of colonies in the lung. These findings indicated the antimetastasis activity of 22-(4'-py)-JA, which might prove useful for further clinical applications.
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Affiliation(s)
- Iksen Iksen
- Department
of Pharmacology and Physiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Suthasinee Seephan
- Pharmaceutical
Sciences and Technology Program, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Vudhiporn Limprasutr
- Department
of Pharmacology and Physiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
- Preclinical
Toxicity and Efficacy Assessment of Medicines and Chemicals Research
Unit, Chulalongkorn University, Bangkok 10330, Thailand
| | - Suwimon Sinsook
- Pharmaceutical
Sciences and Technology Program, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
- Department
of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical
Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Koonchira Buaban
- Department
of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical
Sciences, Chulalongkorn University, Bangkok 10330, Thailand
- Natural
Products and Nanoparticles Research Unit (NP2), Chulalongkorn University, Bangkok 10330, Thailand
| | - Supakarn Chamni
- Department
of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical
Sciences, Chulalongkorn University, Bangkok 10330, Thailand
- Natural
Products and Nanoparticles Research Unit (NP2), Chulalongkorn University, Bangkok 10330, Thailand
| | - Varisa Pongrakhananon
- Department
of Pharmacology and Physiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
- Preclinical
Toxicity and Efficacy Assessment of Medicines and Chemicals Research
Unit, Chulalongkorn University, Bangkok 10330, Thailand
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26
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Wang C, He F, Sun K, Guo K, Lu S, Wu T, Gao X, Fang M. Identification and characterization of 7-azaindole derivatives as inhibitors of the SARS-CoV-2 spike-hACE2 protein interaction. Int J Biol Macromol 2023:125182. [PMID: 37276898 DOI: 10.1016/j.ijbiomac.2023.125182] [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: 04/09/2023] [Revised: 05/25/2023] [Accepted: 05/30/2023] [Indexed: 06/07/2023]
Abstract
The COVID-19 pandemic, caused by SARS-CoV-2, has become a global public health crisis. The entry of SARS-CoV-2 into host cells is facilitated by the binding of its spike protein (S1-RBD) to the host receptor hACE2. Small molecule compounds targeting S1-RBD-hACE2 interaction could provide an alternative therapeutic strategy sensitive to viral mutations. In this study, we identified G7a as a hit compound that targets the S1-RBD-hACE2 interaction, using high-throughput screening in the SARS2-S pseudovirus model. To enhance the antiviral activity of G7a, we designed and synthesized a series of novel 7-azaindole derivatives that bind to the S1-RBD-hACE2 interface. Surprisingly, ASM-7 showed excellent antiviral activity and low cytotoxicity, as confirmed by pseudovirus and native virus assays. Molecular docking and molecular dynamics simulations revealed that ASM-7 could stably bind to the binding interface of S1-RBD-hACE2, forming strong non-covalent interactions with key residues. Furthermore, the binding of ASM-7 caused alterations in the structural dynamics of both S1-RBD and hACE2, resulting in a decrease in their binding affinity and ultimately impeding the viral invasion of host cells. Our findings demonstrate that ASM-7 is a promising lead compound for developing novel therapeutics against SARS-CoV-2.
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Affiliation(s)
- Chaojie Wang
- School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China
| | - Fengming He
- School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China
| | - Ke Sun
- School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China
| | - Kaiqiang Guo
- School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China
| | - Sheng Lu
- School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China
| | - Tong Wu
- School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China.
| | - Xiang Gao
- School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China.
| | - Meijuan Fang
- School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China.
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27
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Lammi C, Fassi EMA, Manenti M, Brambilla M, Conti M, Li J, Roda G, Camera M, Silvani A, Grazioso G. Computational Design, Synthesis, and Biological Evaluation of Diimidazole Analogues Endowed with Dual PCSK9/HMG-CoAR-Inhibiting Activity. J Med Chem 2023. [PMID: 37261954 DOI: 10.1021/acs.jmedchem.3c00279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Proprotein convertase subtilisin/kexin 9 (PCSK9) is responsible for the degradation of the hepatic low-density lipoprotein receptor (LDLR), which regulates circulating cholesterol levels. Consequently, the PCSK9 inhibition is a valuable therapeutic approach for the treatment of hypercholesterolemia and cardiovascular diseases. In our studies, we discovered Rim13, a polyimidazole derivative reducing the protein-protein interaction between PCSK9 and LDLR with an IC50 of 1.6 μM. The computational design led to the optimization of the shape of the PCSK9/ligand complementarity, enabling the discovery of potent diimidazole derivatives. In fact, carrying out biological assays to fully characterize the cholesterol-lowering activity of the new analogues and using both biochemical and cellular techniques, compound Dim16 displayed improved PCSK9 inhibitory activity (IC50 0.9 nM). Interestingly, similar to other lupin-derived peptides and their synthetic analogues, some compounds in this series showed dual hypocholesterolemic activity since some of them complementarily inhibited the 3-hydroxy-3-methylglutaryl coenzyme A reductase.
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Affiliation(s)
- Carmen Lammi
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milan, Italy
| | - Enrico M A Fassi
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milan, Italy
| | - Marco Manenti
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi 10, 20133 Milan, Italy
| | - Marta Brambilla
- Centro Cardiologico Monzino IRCCS, via Parea 4, 20138 Milan, Italy
| | - Maria Conti
- Centro Cardiologico Monzino IRCCS, via Parea 4, 20138 Milan, Italy
| | - Jianqiang Li
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milan, Italy
| | - Gabriella Roda
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milan, Italy
| | - Marina Camera
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milan, Italy
- Centro Cardiologico Monzino IRCCS, via Parea 4, 20138 Milan, Italy
| | - Alessandra Silvani
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi 10, 20133 Milan, Italy
| | - Giovanni Grazioso
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milan, Italy
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28
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Stampolaki M, Stylianakis I, Zgurskaya HI, Kolocouris A. Study of SQ109 analogs binding to mycobacterium MmpL3 transporter using MD simulations and alchemical relative binding free energy calculations. J Comput Aided Mol Des 2023; 37:245-264. [PMID: 37129848 DOI: 10.1007/s10822-023-00504-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 04/03/2023] [Indexed: 05/03/2023]
Abstract
N-geranyl-N΄-(2-adamantyl)ethane-1,2-diamine (SQ109) is a tuberculosis drug that has high potency against Mycobacterium tuberculosis (Mtb) and may function by blocking cell wall biosynthesis. After the crystal structure of MmpL3 from Mycobacterium smegmatis in complex with SQ109 became available, it was suggested that SQ109 inhibits Mmpl3 mycolic acid transporter. Here, we showed using molecular dynamics (MD) simulations that the binding profile of nine SQ109 analogs with inhibitory potency against Mtb and alkyl or aryl adducts at C-2 or C-1 adamantyl carbon to MmpL3 was consistent with the X-ray structure of MmpL3 - SQ109 complex. We showed that rotation of SQ109 around carbon-carbon bond in the monoprotonated ethylenediamine unit favors two gauche conformations as minima in water and lipophilic solvent using DFT calculations as well as inside the transporter's binding area using MD simulations. The binding assays in micelles suggested that the binding affinity of the SQ109 analogs was increased for the larger, more hydrophobic adducts, which was consistent with our results from MD simulations of the SQ109 analogues suggesting that sizeable C-2 adamantyl adducts of SQ109 can fill a lipophilic region between Y257, Y646, F260 and F649 in MmpL3. This was confirmed quantitatively by our calculations of the relative binding free energies using the thermodynamic integration coupled with MD simulations method with a mean assigned error of 0.74 kcal mol-1 compared to the experimental values.
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Affiliation(s)
- Marianna Stampolaki
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771, Athens, Greece
- Department of NMR-Based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, 37077, Göttingen, Germany
| | - Ioannis Stylianakis
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771, Athens, Greece
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, Stephenson Life Sciences Research Center, 101 Stephenson Parkway, Norman, OK, 73019-5251, USA
| | - Antonios Kolocouris
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771, Athens, Greece.
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Wang S, Luan J, Chen L, Liu H, Li W, Wang J. Computational characteristics of the structure-activity relationship of inhibitors targeting Pks13-TE domain. Comput Biol Chem 2023; 104:107864. [PMID: 37028177 DOI: 10.1016/j.compbiolchem.2023.107864] [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: 02/11/2023] [Revised: 03/22/2023] [Accepted: 04/01/2023] [Indexed: 04/09/2023]
Abstract
Multiple studies have established the Pks13-TE domain as a promising target for anti-tuberculosis drug development. However, recent findings have revealed that the lead compound currently in the pipeline for Pks13-TE has significant cardiotoxicity issues. Given the pressing need for new chemical structures for Pks13-TE inhibitors, this study aims to provide a detailed understanding of the Pks13-TE domain binding site through the application of computational chemical biology techniques. Our results highlight the size and shape of the Pks13-TE domain binding pocket, key residues including Asp1644, Asn1640, Phe1670, and Tyr1674 within the pocket, and inhibitor pharmacophore characteristics such as aromatic ring sites, positively charged sites, and hydrogen bond donors. To our knowledge, these simulation results are novel and contribute to the discovery of next-generation Pks13-TE inhibitors without similar prior studies.
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Affiliation(s)
- Shizun Wang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China; Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University, Shenyang 110016, China; School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Jiasi Luan
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China; Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University, Shenyang 110016, China; School of Medical Devices, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Lu Chen
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China; Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University, Shenyang 110016, China; School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Haihan Liu
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China; Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University, Shenyang 110016, China; School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Weixia Li
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China; Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University, Shenyang 110016, China; School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Jian Wang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China; Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University, Shenyang 110016, China; School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China.
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30
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Patel CN, Mall R, Bensmail H. AI-driven drug repurposing and binding pose meta dynamics identifies novel targets for Monkeypox virus. J Infect Public Health 2023; 16:799-807. [PMID: 36966703 PMCID: PMC10014505 DOI: 10.1016/j.jiph.2023.03.007] [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: 09/20/2022] [Revised: 02/28/2023] [Accepted: 03/05/2023] [Indexed: 03/17/2023] Open
Abstract
Monkeypox virus (MPXV) was confirmed in May 2022 and designated a global health emergency by WHO in July 2022. MPX virions are big, enclosed, brick-shaped, and contain a linear, double-stranded DNA genome as well as enzymes. MPXV particles bind to the host cell membrane via a variety of viral-host protein interactions. As a result, the wrapped structure is a potential therapeutic target. DeepRepurpose, an artificial intelligence-based compound-viral proteins interaction framework, was used via a transfer learning setting to prioritize a set of FDA approved and investigational drugs which can potentially inhibit MPXV viral proteins. To filter and narrow down the lead compounds from curated collections of pharmaceutical compounds, we used a rigorous computational framework that included homology modeling, molecular docking, dynamic simulations, binding free energy calculations, and binding pose metadynamics. We identified Elvitegravir as a potential inhibitor of MPXV virus using our comprehensive pipeline.
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Affiliation(s)
- Chirag N. Patel
- Department of Botany, Bioinformatics and Climate Change Impacts Management, School of Science, Gujarat University, Ahmedabad-380009, India,Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institute of Health, Frederick, MD-21702, USA
| | - Raghvendra Mall
- Department of Immunology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee-38105, USA,Biotechnology Research Center, Technology Innovation Institute, Abu Dhabi-9639, United Arab Emirates,Corresponding author at: Department of Immunology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee-38105, USA
| | - Halima Bensmail
- Qatar Computing Research Institute, Hamad Bin Khalifa University, Doha-34110, Qatar,Corresponding author
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31
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He F, Wang X, Wu Q, Liu S, Cao Y, Guo X, Yin S, Yin N, Li B, Fang M. Identification of potential ATP-competitive cyclin-dependent kinase 1 inhibitors: De novo drug generation, molecular docking, and molecular dynamics simulation. Comput Biol Med 2023; 155:106645. [PMID: 36774892 DOI: 10.1016/j.compbiomed.2023.106645] [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: 11/16/2022] [Revised: 01/27/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023]
Abstract
Cyclin-dependent kinases 1 (CDK1) has been identified as a potential target for the search for new antitumor drugs. However, no clinically effective CDK1 inhibitors are now available for cancer treatment. Therefore, this study aimed to offer potential CDK1 inhibitors using de novo drug generation, molecular docking, and molecular dynamics (MD) simulation studies. We first utilized the BREED algorithm (a de novo drug generation approach) to produce a novel library of small molecules targeting CDK1. To initially obtain novel potential CDK1 inhibitors with favorable physicochemical properties and excellent druggability, we performed a virtual rule-based rational drug screening on our generated library and found ten initial hits. Then, the molecular interactions and dynamic stability of these ten initial hits and CDK1 complexes during their all-atom MD simulations (total 18 μs) and binding pose metadynamics simulations were investigated, resulting in five final hits. Furthermore, another MD simulation (total 2.1 μs) with different force fields demonstrated the binding ability of the five hits to CDK1. It was found that these five hits, CBMA001 (ΔG = -29.88 kcal/mol), CBMA002 (ΔG = -34.89 kcal/mol), CBMA004 (ΔG = -32.47 kcal/mol), CBMA007 (ΔG = -31.16 kcal/mol), and CBMA008 (ΔG = -34.78 kcal/mol) possessed much greater binding affinity to CDK1 than positive compound Flavopiridol (FLP, ΔG = -25.38 kcal/mol). Finally, CBMA002 and CBMA004 were identified as excellent selective CDK1 inhibitors in silico. Together, this study provides a workflow for rational drug design and two promising selective CDK1 inhibitors that deserve further investigation.
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Affiliation(s)
- Fengming He
- Fujian Provincial Key Laboratory of Innovative Drug Target Research and State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, 361102, China
| | - Xiumei Wang
- Fujian Provincial Key Laboratory of Innovative Drug Target Research and State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, 361102, China
| | - Qiaoqiong Wu
- Fujian Provincial Key Laboratory of Innovative Drug Target Research and State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, 361102, China
| | - Shunzhi Liu
- Fujian Provincial Key Laboratory of Innovative Drug Target Research and State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, 361102, China
| | - Yin Cao
- Fujian Provincial Key Laboratory of Innovative Drug Target Research and State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, 361102, China
| | - Xiaodan Guo
- Fujian Provincial Key Laboratory of Innovative Drug Target Research and State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, 361102, China
| | - Sihang Yin
- Fujian Provincial Key Laboratory of Innovative Drug Target Research and State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, 361102, China
| | - Na Yin
- School of Pharmaceutical Sciences, Sun Yat-Sen University, University Town, Guangzhou, 510006, China
| | - Baicun Li
- National Center for Respiratory Medicine Laboratories, Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, 100029, China; National Clinical Research Center for Respiratory Diseases, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, 100029, China.
| | - Meijuan Fang
- Fujian Provincial Key Laboratory of Innovative Drug Target Research and State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, 361102, China.
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32
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Yu Y, Xu S, He R, Liang G. Application of Molecular Simulation Methods in Food Science: Status and Prospects. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:2684-2703. [PMID: 36719790 DOI: 10.1021/acs.jafc.2c06789] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Molecular simulation methods, such as molecular docking, molecular dynamic (MD) simulation, and quantum chemical (QC) calculation, have become popular as characterization and/or virtual screening tools because they can visually display interaction details that in vitro experiments can not capture and quickly screen bioactive compounds from large databases with millions of molecules. Currently, interdisciplinary research has expanded molecular simulation technology from computer aided drug design (CADD) to food science. More food scientists are supporting their hypotheses/results with this technology. To understand better the use of molecular simulation methods, it is necessary to systematically summarize the latest applications and usage trends of molecular simulation methods in the research field of food science. However, this type of review article is rare. To bridge this gap, we have comprehensively summarized the principle, combination usage, and application of molecular simulation methods in food science. We also analyzed the limitations and future trends and offered valuable strategies with the latest technologies to help food scientists use molecular simulation methods.
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Affiliation(s)
- Yuandong Yu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing400030, China
| | - Shiqi Xu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing400030, China
| | - Ran He
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing400030, China
| | - Guizhao Liang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing400030, China
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33
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Computational Approaches to the Rational Design of Tubulin-Targeting Agents. Biomolecules 2023; 13:biom13020285. [PMID: 36830654 PMCID: PMC9952983 DOI: 10.3390/biom13020285] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Microtubules are highly dynamic polymers of α,β-tubulin dimers which play an essential role in numerous cellular processes such as cell proliferation and intracellular transport, making them an attractive target for cancer and neurodegeneration research. To date, a large number of known tubulin binders were derived from natural products, while only one was developed by rational structure-based drug design. Several of these tubulin binders show promising in vitro profiles while presenting unacceptable off-target effects when tested in patients. Therefore, there is a continuing demand for the discovery of safer and more efficient tubulin-targeting agents. Since tubulin structural data is readily available, the employment of computer-aided design techniques can be a key element to focus on the relevant chemical space and guide the design process. Due to the high diversity and quantity of structural data available, we compiled here a guide to the accessible tubulin-ligand structures. Furthermore, we review different ligand and structure-based methods recently used for the successful selection and design of new tubulin-targeting agents.
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34
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Insights into the inhibitory activity and mechanism of action of flavonoids from the stems and branches of Acer mono Maxim. against α-glucosidase via kinetic analysis, molecular docking, and molecular dynamics simulations. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
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35
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Caboni P, Laus A, Eloh K, Ntalli NG, Casula M, Di Giorgi S, Tocco G. Structural Elucidation of Relevant Gibberellic Acid Impurities and In Silico Investigation of Their Interaction with Soluble Gibberellin Receptor GID1. ACS OMEGA 2023; 8:1957-1966. [PMID: 36687088 PMCID: PMC9850740 DOI: 10.1021/acsomega.2c04743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
Gibberellin derivatives are a family of tetracyclic diterpenoid plant hormones used in agriculture as plant growth regulators included in the European Directive 91/414. In the pesticide peer review process and to assess their toxicological relevance and product chemical equivalence, the European Food Safety Authority (EFSA) highlighted data gaps such as the identification of hydrolysis products and unknown impurities. The aspect of impurity characterization and quantitation is challenging and requires the use of hyphenated analytical techniques. In this regard, we used an LC-QTOF/MS and NMR analysis for the characterization of gibberellic acid impurities found in technical products. Gibberellic acid impurities such as gibberellin A1 (GA 1 ), 3-isolactone gibberellic acid (iso-GA 3 ), gibberellenic acid, 1α,2α-epoxygibberellin A3 (2-epoxy- GA 3 ), and (1α,2β,3α,4bβ,10β)-2,3,7-trihydroxy-1-methyl-8-methylenegibb-4-ene-1,10-dicarboxylic acid were identified and successfully characterized. Moreover, an in silico investigation on selected gibberellic acid impurities and derivatives and their interactions with a gibberellin insensitive dwarf1 (GID1) receptor has been carried out by means of induced fit docking (IFD), generalized-Born surface area (MM-GBSA), and metadynamics (MTD) experiments. A direct HPLC method with DAD and MS for the detection of gibberellic acid and its impurities in a technical sample has been developed. Moreover, by means of the in silico characterization of the GID1 receptor-binding pocket, we investigated the receptor affinity of the selected gibberellins, identifying compounds (2) and (4) as the most promising hit to lead compounds.
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Affiliation(s)
- Pierluigi Caboni
- Department
of Life and Environmental Sciences, Cittadella
Universitaria di Monserrato, Blocco A, 09042, Monserrato, Italy
| | - Antonio Laus
- Department
of Biomedical Sciences, Cittadella Universitaria
di Monserrato, Blocco
A, 09042, Monserrato, Italy
| | - Kodjo Eloh
- University
of Kara, Po Box 404 Kara, Togo
| | - Nikoletta G. Ntalli
- Department
of Pesticides Control and Phytopharmacy, Benaki Phytopathological Institute, 8 S. Delta Str., 14561 Athens, Greece
| | - Mattia Casula
- Department
of Life and Environmental Sciences, Cittadella
Universitaria di Monserrato, Blocco A, 09042, Monserrato, Italy
| | - Sabrina Di Giorgi
- Ministero
della Salute, Direzione Generale per l’Igiene
e la Sicurezza degli Alimenti e della Nutrizione, Viale Giorgio Ribotta, 5, 00144 Roma, Italy
| | - Graziella Tocco
- Department
of Life and Environmental Sciences, Cittadella
Universitaria di Monserrato, Blocco A, 09042, Monserrato, Italy
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36
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Gholami A, Minai-Tehrani D, Eriksson LA. In silico and in vitro studies confirm Ondansetron as a novel acetylcholinesterase and butyrylcholinesterase inhibitor. Sci Rep 2023; 13:643. [PMID: 36635365 PMCID: PMC9837033 DOI: 10.1038/s41598-022-27149-z] [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: 09/26/2022] [Accepted: 12/27/2022] [Indexed: 01/14/2023] Open
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder that is growing rapidly among the elderly population around the world. Studies show that a lack of acetylcholine and butyrylcholine due to the overexpression of enzymes Acetylcholinesterase (AChE) and Butyrylcholinesterase (BChE) may lead to reduced communication between neuron cells. As a result, seeking novel inhibitors targeting these enzymes might be vital for the future treatment of AD. Ondansetron is used to prevent nausea and vomiting caused by chemotherapy or radiation treatments and is herein shown to be a potent inhibitor of cholinesterase. Comparison is made between Ondansetron and FDA-approved cholinesterase inhibitors Rivastigmine and Tacrine. Molecular docking demonstrates that interactions between the studied ligand and aromatic residues in the peripheral region of the active site are important in binding. Molecular dynamics simulations and binding pose metadynamics show that Ondansetron is highly potent against both enzymes and far better than Rivastigmine. Inhibitor activities evaluated by in vitro studies confirm that the drug inhibits AChE and BChE by non-competitive and mixed inhibition, respectively, with IC50 values 33 µM (AChE) and 2.5 µM (BChE). Based on the findings, we propose that Ondansetron may have therapeutic applications in inhibiting cholinesterase, especially for BChE.
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Affiliation(s)
- Asma Gholami
- Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30, Göteborg, Sweden
| | - Dariush Minai-Tehrani
- Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran.
| | - Leif A Eriksson
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30, Göteborg, Sweden.
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37
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Thirunavukkarasu MK, Karuppasamy R. Drug repurposing combined with MM/PBSA based validation strategies towards MEK inhibitors screening. J Biomol Struct Dyn 2022; 40:12392-12403. [PMID: 34459701 DOI: 10.1080/07391102.2021.1970629] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Emergence of oncogenic mutations in the MAPK pathway gaining more impact in the recent years. Importantly, MEK is a core element of this pathway as it is easy to inhibit and is a gatekeeper of multiple malignancies. Therefore, we performed in-silico strategy to screen repurposed candidate for MEK protein using a library of 11,808 compounds from different clusters in the DrugBank database. Glide docking, Prime-MM/GBSA and QikProp analysis were implemented to retrieve the hits with high precision. The stability of the binding mode and binding affinity of the resultant hit were explored using molecular dynamic simulations and MM/PBSA approach. The results highlight that Nebivolol (DB04861) not only achieved a stable conformation in the MEK binding pocket but also displayed highest binding affinity than the other molecules investigated in our study. Taken together, we hypothesized that Nebivolol is an excellent candidate for the inhibition of MEK in NSCLC patients in future.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Muthu Kumar Thirunavukkarasu
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Ramanathan Karuppasamy
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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38
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Lukauskis D, Samways ML, Aureli S, Cossins BP, Taylor RD, Gervasio FL. Open Binding Pose Metadynamics: An Effective Approach for the Ranking of Protein-Ligand Binding Poses. J Chem Inf Model 2022; 62:6209-6216. [PMID: 36401553 DOI: 10.1021/acs.jcim.2c01142] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Predicting the correct pose of a ligand binding to a protein and its associated binding affinity is of great importance in computer-aided drug discovery. A number of approaches have been developed to these ends, ranging from the widely used fast molecular docking to the computationally expensive enhanced sampling molecular simulations. In this context, methods such as coarse-grained metadynamics and binding pose metadynamics (BPMD) use simulations with metadynamics biasing to probe the binding affinity without trying to fully converge the binding free energy landscape in order to decrease the computational cost. In BPMD, the metadynamics bias perturbs the ligand away from the initial pose. The resistance of the ligand to this bias is used to calculate a stability score. The method has been shown to be useful in reranking predicted binding poses from docking. Here, we present OpenBPMD, an open-source Python reimplementation and reinterpretation of BPMD. OpenBPMD is powered by the OpenMM simulation engine and uses a revised scoring function. The algorithm was validated by testing it on a wide range of targets and showing that it matches or exceeds the performance of the original BPMD. We also investigated the role of accurate water positioning on the performance of the algorithm and showed how the combination with a grand-canonical Monte Carlo algorithm improves the accuracy of the predictions.
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Affiliation(s)
- Dominykas Lukauskis
- Department of Chemistry, University College London, LondonWC1E 6BT, United Kingdom
| | | | - Simone Aureli
- Biomolecular and Pharmaceutical Modelling Group, School of Pharmaceutical Sciences, University of Geneva, CH1211Geneva, Switzerland.,Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), University of Geneva, CH1211Geneva, Switzerland
| | - Benjamin P Cossins
- UCB, 216 Bath Road, SloughSL1 3WE, United Kingdom.,Exscientia Ltd., The Schrödinger Building, Oxford Science Park, OxfordOX4 4GE, United Kingdom
| | | | - Francesco Luigi Gervasio
- Department of Chemistry, University College London, LondonWC1E 6BT, United Kingdom.,Biomolecular and Pharmaceutical Modelling Group, School of Pharmaceutical Sciences, University of Geneva, CH1211Geneva, Switzerland.,Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), University of Geneva, CH1211Geneva, Switzerland.,UCB, 216 Bath Road, SloughSL1 3WE, United Kingdom
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39
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Yang Z, Wang W, Qi Y, Yang Y, Chen CH, Liu JZ, Chu GX, Bao GH. Exploring new catechin derivatives as SARS-CoV-2 M pro inhibitors from tea by molecular networking, surface plasma resonance, enzyme inhibition, induced fit docking, and metadynamics simulations. Comput Biol Med 2022; 151:106288. [PMID: 36401970 PMCID: PMC9652097 DOI: 10.1016/j.compbiomed.2022.106288] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/23/2022] [Accepted: 11/06/2022] [Indexed: 11/13/2022]
Abstract
SARS-CoV-2 Mpro (Mpro) is the critical cysteine protease in coronavirus viral replication. Tea polyphenols are effective Mpro inhibitors. Therefore, we aim to isolate and synthesize more novel tea polyphenols from Zhenghedabai (ZHDB) white tea methanol-water (MW) extracts that might inhibit COVID-19. Through molecular networking, 33 compounds were identified and divided into 5 clusters. Further, natural products molecular network (MN) analysis showed that MN1 has new phenylpropanoid-substituted ester-catechin (PSEC), and MN5 has the important basic compound type hydroxycinnamoylcatechins (HCCs). Thus, a new PSEC (1, PSEC636) was isolated, which can be further detected in 14 green tea samples. A series of HCCs were synthesized (2-6), including three new acetylated HCCs (3-5). Then we used surface plasmon resonance (SPR) to analyze the equilibrium dissociation constants (KD) for the interaction of 12 catechins and Mpro. The KD values of PSEC636 (1), EGC-C (2), and EC-CDA (3) were 2.25, 2.81, and 2.44 μM, respectively. Moreover, compounds 1, 2, and 3 showed the potential Mpro inhibition with IC50 5.95 ± 0.17, 9.09 ± 0.22, and 23.10 ± 0.69 μM, respectively. Further, we used induced fit docking (IFD), binding pose metadynamics (BPMD), and molecular dynamics (MD) to explore the stable binding pose of Mpro-1, showing that 1 could tightly bond with the amino acid residues THR26, HIS41, CYS44, TYR54, GLU166, and ASP187. The computer modeling studies reveal that the ester, acetyl, and pyrogallol groups could improve inhibitory activity. Our research suggests that these catechins are effective Mpro inhibitors, and might be developed as therapeutics against COVID-19.
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Affiliation(s)
- Zi Yang
- Natural Products Laboratory, State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Wei Wang
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Medicine Resources, West Anhui University, Lu'an, Anhui, 237012, China
| | - Yan Qi
- Natural Products Laboratory, State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Yi Yang
- Natural Products Laboratory, State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Chen-Hui Chen
- Natural Products Laboratory, State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Jia-Zheng Liu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease, Macau University of Science and Technology, Taipa, 999078, Macau
| | - Gang-Xiu Chu
- School of Information and Computer, Anhui Agricultural University, Hefei, Anhui, 230036, China,Corresponding author
| | - Guan-Hu Bao
- Natural Products Laboratory, State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui, 230036, China,Corresponding author
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Sen S, Spasic A, Sinha A, Wang J, Bush M, Li J, Nešić D, Zhou Y, Angiulli G, Morgan P, Salas-Estrada L, Takagi J, Walz T, Coller BS, Filizola M. Structure-Based Discovery of a Novel Class of Small-Molecule Pure Antagonists of Integrin αVβ3. J Chem Inf Model 2022; 62:5607-5621. [PMID: 36279366 PMCID: PMC9767310 DOI: 10.1021/acs.jcim.2c00999] [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] [Indexed: 12/13/2022]
Abstract
Inhibitors of integrin αVβ3 have therapeutic promise for a variety of diseases. Most αVβ3-targeting small molecules patterned after the RGD motif are partial agonists because they induce a high-affinity, ligand-binding conformation and prime the receptor to bind the ligand without an activating stimulus, in part via a charge-charge interaction between their aspartic acid carboxyl group and the metal ion in the metal-ion-dependent adhesion site (MIDAS). Building upon our previous studies on the related integrin αIIbβ3, we searched for pure αVβ3 antagonists that lack this typical aspartic acid carboxyl group and instead engage through direct binding to one of the coordinating residues of the MIDAS metal ion, specifically β3 E220. By in silico screening of two large chemical libraries for compounds interacting with β3 E220, we indeed discovered a novel molecule that does not contain an acidic carboxyl group and does not induce the high-affinity, ligand-binding state of the receptor. Functional and structural characterization of a chemically optimized version of this compound led to the discovery of a novel small-molecule pure αVβ3 antagonist that (i) does not prime the receptor to bind the ligand and does not induce hybrid domain swing-out or receptor extension as judged by antibody binding and negative-stain electron microscopy, (ii) binds at the RGD-binding site as predicted by metadynamics rescoring of induced-fit docking poses and confirmed by a cryo-electron microscopy structure of the compound-bound integrin, and (iii) coordinates the MIDAS metal ion via a quinoline moiety instead of an acidic carboxyl group.
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Affiliation(s)
- Soumyo Sen
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1677, New York, New York10029, United States
| | - Aleksandar Spasic
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1677, New York, New York10029, United States
| | - Anjana Sinha
- Allen and Frances Adler Laboratory of Blood and Vascular Biology, The Rockefeller University, 1230 York Avenue, P.O. Box 309, New York, New York10065, United States
| | - Jialing Wang
- Laboratory of Molecular Electron Microscopy, The Rockefeller University, 1230 York Avenue, P.O. Box 219, New York, New York10065, United States
| | - Martin Bush
- Laboratory of Molecular Electron Microscopy, The Rockefeller University, 1230 York Avenue, P.O. Box 219, New York, New York10065, United States
| | - Jihong Li
- Allen and Frances Adler Laboratory of Blood and Vascular Biology, The Rockefeller University, 1230 York Avenue, P.O. Box 309, New York, New York10065, United States
| | - Dragana Nešić
- Allen and Frances Adler Laboratory of Blood and Vascular Biology, The Rockefeller University, 1230 York Avenue, P.O. Box 309, New York, New York10065, United States
| | - Yuchen Zhou
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1677, New York, New York10029, United States
| | - Gabriella Angiulli
- Laboratory of Molecular Electron Microscopy, The Rockefeller University, 1230 York Avenue, P.O. Box 219, New York, New York10065, United States
| | - Paul Morgan
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1677, New York, New York10029, United States
| | - Leslie Salas-Estrada
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1677, New York, New York10029, United States
| | - Junichi Takagi
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka565-0871, Japan
| | - Thomas Walz
- Laboratory of Molecular Electron Microscopy, The Rockefeller University, 1230 York Avenue, P.O. Box 219, New York, New York10065, United States
| | - Barry S Coller
- Allen and Frances Adler Laboratory of Blood and Vascular Biology, The Rockefeller University, 1230 York Avenue, P.O. Box 309, New York, New York10065, United States
| | - Marta Filizola
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1677, New York, New York10029, United States
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41
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Ahmad F, Lakshmi PTV, Arunachalam A. An in silico comparative study of curcumin and 2-deoxyuridine nucleoside derivatives: Reveals the role of angiogenin in ER stress-induced apoptosis signaling. Chem Biol Drug Des 2022; 101:1048-1081. [PMID: 36412086 DOI: 10.1111/cbdd.14184] [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: 10/31/2021] [Revised: 09/06/2022] [Accepted: 11/16/2022] [Indexed: 11/23/2022]
Abstract
Angiogenin (ANG) protein plays a crucial role in angiogenesis, neovascularization, and cancer metastasis in NSCLC (non-small cell lung cancer) via non-coding tiRNA. It protects the cell under ER (endoplasmic reticulum) stress-induced apoptosis through the translational reprogramming process. Although B82 (Curcumin derivatives) induces ER stress-induced apoptosis, its mechanism of action was not studied. Therefore, it was hypothesized that the ribonucleolytic activity of ANG may be regulated by B82, resulting in modulated ER stress signaling for apoptosis. Hence, we designed and proposed a synthesis scheme for RNA-based anti-angiogenic derivatives of 2-deoxyuridine nucleoside forming peptide bond with amino acids like serine (Ser-3) and para-hydroxy-phenyl glycine (Normtyr-1) and compared B82 with them to know the binding affinity with ANG, anti-angiogenic potential, and its probable mechanism of anti-RNase activity through MD simulation study. Therefore, using Gromos96 43a1 and 43a2 force fields, MD simulation was performed to investigate binding affinity, ligand-induced molecular surface area change, conformational change, and dynamics of catalytic site residues to predict ligand binding to ANG in this study. The obtained binding free energy (∆Gbind ) result showed the total average ∆Gbind as -113.480 ± 1.682 (Normtyr-1) > -53.038 ± 33.069 (B82) > -27.909 ± 16.438 (Ser-3) kJ/mole specify role of B82 in regulating ER stress signaling induced apoptosis through ANG ribonucleolytic activity inhibition, suitability of 43a2 force fields and methodology in ligand screening. It shows the crucial role of Leu115 and His13 residue involvement in total ∆Gbind contribution. Hence, based on the MD result, novel conformation of catalytic residues, and ∆Gbind , a promising combination candidate could be proposed for metastatic NSCLC therapy.
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Affiliation(s)
- Faizan Ahmad
- Department of Bioinformatics, Pondicherry University, Pondicherry, India
| | | | - Annamalai Arunachalam
- PG and Research Department of Botany Arignar Anna Government Arts College Villupuram Tamil Nadu India
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Manish M, Mishra S, Anand A, Subbarao N. Computational molecular interaction between SARS-CoV-2 main protease and theaflavin digallate using free energy perturbation and molecular dynamics. Comput Biol Med 2022; 150:106125. [PMID: 36240593 PMCID: PMC9507791 DOI: 10.1016/j.compbiomed.2022.106125] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 09/10/2022] [Accepted: 09/18/2022] [Indexed: 12/04/2022]
Abstract
Our objective was to identify the molecule which can inhibit SARS-CoV-2 main protease and can be easily procured. Natural products may provide such molecules and can supplement the current custom chemical synthesis-based drug discovery for this objective. A combination of docking approaches, scoring functions, classical molecular dynamic simulation, binding pose metadynamics, and free energy perturbation calculations have been employed in this study. Theaflavin digallate has been observed in top-scoring compounds after the three independent virtual screening simulations of 598435 compounds (unique 27256 chemical entities). The main protease-theaflavin digallate complex interacts with critical active site residues of the main protease in molecular dynamics simulation independent of the explored computational framework, simulation time, initial structure, and force field used. Theaflavin digallate forms approximately three hydrogen bonds with Glutamate166 of main protease, primarily through hydroxyl groups in the benzene ring of benzo(7)annulen-6-one, along with other critical residues. Glu166 is the most critical amino acid for main protease dimerization, which is necessary for catalytic activity. The estimated binding free energy, calculated by Amber and Schrodinger MMGBSA module, reflects a high binding free energy between theaflavin digallate and main protease. Binding pose metadynamics simulation shows the highly persistent H-bond and a stable pose for the theaflavin digallate-main protease complex. Using method control, experimental controls, and test set, alchemical transformation studies confirm high relative binding free energy of theaflavin digallate with the main protease. Computational molecular interaction suggests that theaflavin digallate can inhibit the main protease of SARS-CoV-2.
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Affiliation(s)
- Manish Manish
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India.
| | - Smriti Mishra
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India.
| | - Ayush Anand
- BP Koirala Institute of Health Sciences, Dharan, Nepal.
| | - Naidu Subbarao
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India.
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De Luca MA, Tocco G, Mostallino R, Laus A, Caria F, Musa A, Pintori N, Ucha M, Poza C, Ambrosio E, Di Chiara G, Castelli MP. Pharmacological characterization of novel synthetic opioids: Isotonitazene, metonitazene, and piperidylthiambutene as potent MU opioid receptor agonists. Neuropharmacology 2022; 221:109263. [PMID: 36154843 DOI: 10.1016/j.neuropharm.2022.109263] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 09/07/2022] [Accepted: 09/17/2022] [Indexed: 11/30/2022]
Abstract
Recent trends of opioid abuse and related fatalities have highlighted the critical role of Novel Synthetic Opioids (NSOs). We studied the μ-opioid-like properties of isotonitazene (ITZ), metonitazene (MTZ), and piperidylthiambutene (PTB) using different approaches. In vitro studies showed that ITZ and MTZ displayed a higher potency in both rat membrane homogenates (EC50: 0.99 and 19.1 nM, respectively) and CHO-MOR (EC50: 0.71 and 10.0 nM, respectively) than [D-Ala2, NMe-Phe4, Gly-ol5]-enkephalin (DAMGO), with no difference in maximal efficacy (Emax) between DAMGO and NSOs. ITZ also has higher affinity (Ki: 0.06 and 0.05 nM) at the MOR than DAMGO in both systems, whilst MTZ has higher affinity in CHO-MOR (Ki = 0.23 nM) and similar affinity in rat cerebral cortex (Ki = 0.22 nM). PTB showed lower affinity and potency than DAMGO. In vivo, ITZ displayed higher analgesic potency than fentanyl and morphine (ED50: 0.00156, 0.00578, 2.35 mg/kg iv, respectively); ITZ (0.01 mg/kg iv) and MTZ (0.03 mg/kg iv) reduced behavioral activity and increased dialysate dopamine (DA) in the NAc shell (max. about 200% and 170% over basal value, respectively. Notably, ITZ elicited an increase in DA comparable to that of higher dose of morphine (1 mg/kg iv), but higher than the same dose of fentanyl (0.01 mg/kg iv). In silico, induced fit docking (IFD) and metadynamic simulations (MTD) showed that binding modes and structural changes at the receptor, ligand stability, and the overall energy score of NSOs were consistent with the results of the biological assays.
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Affiliation(s)
| | - Graziella Tocco
- Department of Life and Environmental Sciences, University of Cagliari, Italy
| | | | - Antonio Laus
- Department of Life and Environmental Sciences, University of Cagliari, Italy
| | - Francesca Caria
- Department of Biomedical Sciences, University of Cagliari, Italy
| | - Aurora Musa
- Department of Biomedical Sciences, University of Cagliari, Italy
| | - Nicholas Pintori
- Department of Biomedical Sciences, University of Cagliari, Italy
| | - Marcos Ucha
- Department of Psychobiology, National University for Distance Learning (UNED), Madrid, Spain
| | - Celia Poza
- Department of Psychobiology, National University for Distance Learning (UNED), Madrid, Spain
| | - Emilio Ambrosio
- Department of Psychobiology, National University for Distance Learning (UNED), Madrid, Spain
| | - Gaetano Di Chiara
- Department of Biomedical Sciences, University of Cagliari, Italy; CNR Institute of Neuroscience, Cagliari Section, University of Cagliari, Italy.
| | - M Paola Castelli
- Department of Biomedical Sciences, University of Cagliari, Italy.
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Chahal V, Kakkar R. A combination strategy of structure-based virtual screening, MM-GBSA, cross docking, molecular dynamics and metadynamics simulations used to investigate natural compounds as potent and specific inhibitors of tumor linked human carbonic anhydrase IX. J Biomol Struct Dyn 2022:1-16. [PMID: 35735269 DOI: 10.1080/07391102.2022.2087736] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Cancer remains a serious health concern representing one of the leading causes of deaths worldwide. The enzyme human carbonic anhydrase IX (hCA IX) is found to be over-expressed in many cancer types and its selective inhibition over its cytosolic off-target isoform, human carbonic anhydrase II (hCA II), represents a potential area of research in the development of novel anticancer compounds. This work is concerned with the use of various in silico tools for the identification of natural product based molecules that can selectively inhibit hCA IX over hCA II. MM-GBSA assisted structure-based virtual screening against hCA IX was performed for nearly 225,000 natural products imported from the ZINC15 database. The obtained hits were checked for their potency by considering acetazolamide, the bound inhibitor of hCA IX, as the reference molecule, and 121 molecules were identified as potent hCA IX inhibitors. After ensuring their potency, cross-docking, followed by MM-GBSA calculations of the hits with hCA II, was performed, and their selectivity was assessed by considering the hCA IX selective compound SLC-0111 as the reference molecule, and 50 natural products were identified as potent as well as selective hCA IX inhibitors. Molecules with the quinoline scaffold showed the highest selectivity, and their selectivity was attributed to the strong electrostatic interactions of the zinc binding group (ZBG) with the active site Zn(II) ion. Furthermore, the stability of the binding modes of the top hCA IX selective hits was ensured by performing molecular dynamics (MD) simulations, which clearly proved that one of the short-listed molecules is truly selective, as it does not interact with the active site Zn(II) ion of hCA II, but interacts strongly with this ion in hCA IX. Bonding pose metadynamics studies revealed that the ligand moves to a more stable binding site from the one predicted by the docking studies and shows stronger interaction with the protein and Zn(II) at this binding site. The ligand is not likely to have issues with bioavailability. As a result, this ligand can be taken for bioassay testing and subsequently used as a feasible therapeutic treatment for a variety of cancer types. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Varun Chahal
- Computational Chemistry Group, Department of Chemistry, University of Delhi, Delhi, India
| | - Rita Kakkar
- Computational Chemistry Group, Department of Chemistry, University of Delhi, Delhi, India
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Kandi V, Vundecode A, Godalwar TR, Dasari S, Vadakedath S, Godishala V. The Current Perspectives in Clinical Research: Computer-Assisted Drug Designing, Ethics, and Good Clinical Practice. BORNEO JOURNAL OF PHARMACY 2022. [DOI: 10.33084/bjop.v5i2.3013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
In the era of emerging microbial and non-communicable diseases and re-emerging microbial infections, the medical fraternity and the public are plagued by under-preparedness. It is evident by the severity of the Coronavirus disease (COVID-19) pandemic that novel microbial diseases are a challenge and are challenging to control. This is mainly attributed to the lack of complete knowledge of the novel microbe’s biology and pathogenesis and the unavailability of therapeutic drugs and vaccines to treat and control the disease. Clinical research is the only answer utilizing which can handle most of these circumstances. In this review, we highlight the importance of computer-assisted drug designing (CADD) and the aspects of molecular docking, molecular superimposition, 3D-pharmacophore technology, ethics, and good clinical practice (GCP) for the development of therapeutic drugs, devices, and vaccines.
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Identification of Potential WSB1 Inhibitors by AlphaFold Modeling, Virtual Screening, and Molecular Dynamics Simulation Studies. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:4629392. [PMID: 35600960 PMCID: PMC9122669 DOI: 10.1155/2022/4629392] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 04/27/2022] [Indexed: 12/03/2022]
Abstract
WD40 repeat and SOCS box containing 1 (WSB1) consists of seven WD40 repeat structural domains at the N-terminal end and one SOCS box structural domain at the C-terminal end. WSB1 promotes cancer progression by affecting the Von Hippel–Lindau tumor suppressor protein (pVHL) and upregulating hypoxia inducible factor-1α (HIF-1α) target gene expression. However, the crystal structure of WSB1 has not been reported, which is not beneficial to the research on WSB1 inhibitors. Therefore, we focused on specific small molecule inhibitors of WSB1. This study applied virtual screening and molecular dynamics simulations; finally, 20 compounds were obtained. Among them, compound G490-0341 showed the best stable structure and was a promising composite for further development of WSB1 inhibitors.
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47
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Boichuk S, Syuzov K, Bikinieva F, Galembikova A, Zykova S, Gankova K, Igidov S, Igidov N. Computational-Based Discovery of the Anti-Cancer Activities of Pyrrole-Based Compounds Targeting the Colchicine-Binding Site of Tubulin. Molecules 2022; 27:2873. [PMID: 35566235 PMCID: PMC9101527 DOI: 10.3390/molecules27092873] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 04/27/2022] [Accepted: 04/29/2022] [Indexed: 12/10/2022] Open
Abstract
Despite the tubulin-binding agents (TBAs) that are widely used in the clinic for cancer therapy, tumor resistance to TBAs (both inherited and acquired) significantly impairs their effectiveness, thereby decreasing overall survival (OS) and progression-free survival (PFS) rates, especially for the patients with metastatic, recurrent, and unresectable forms of the disease. Therefore, the development of novel effective drugs interfering with the microtubules' dynamic state remains a big challenge in current oncology. We report here about the novel ethyl 2-amino-1-(furan-2-carboxamido)-5-(2-aryl/tert-butyl-2-oxoethylidene)-4-oxo-4,5-dihydro-1H-pyrrole-3-carboxylates (EAPCs) exhibiting potent anti-cancer activities against the breast and lung cancer cell lines in vitro. This was due to their ability to inhibit tubulin polymerization and induce cell cycle arrest in M-phase. As an outcome, the EAPC-treated cancer cells exhibited a significant increase in apoptosis, which was evidenced by the expression of cleaved forms of PARP, caspase-3, and increased numbers of Annexin-V-positive cells. By using the in silico molecular modeling methods (e.g., induced-fit docking, binding metadynamics, and unbiased molecular dynamics), we found that EAPC-67 and -70 preferentially bind to the colchicine-binding site of tubulin. Lastly, we have shown that the EAPCs indicated above and colchicine utilizes a similar molecular mechanism to inhibit tubulin polymerization via targeting the T7 loop in the β-chain of tubulin, thereby preventing the conformational changes in the tubulin dimers required for their polymerization. Collectively, we identified the novel and potent TBAs that bind to the colchicine-binding site and disrupt the microtubule network. As a result of these events, the compounds induced a robust cell cycle arrest in M-phase and exhibited potent pro-apoptotic activities against the epithelial cancer cell lines in vitro.
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Affiliation(s)
- Sergei Boichuk
- Department of Pathology, Kazan State Medical University, 420012 Kazan, Russia; (K.S.); (F.B.); (A.G.)
- Department of Radiotherapy and Radiology, Russian Medical Academy of Continuous Professional Education, 125993 Moscow, Russia
- Biologically Active Terpenoids Laboratory, Kazan Federal University, 18 Kremlyovskaya St., 420008 Kazan, Russia
| | - Kirill Syuzov
- Department of Pathology, Kazan State Medical University, 420012 Kazan, Russia; (K.S.); (F.B.); (A.G.)
| | - Firuza Bikinieva
- Department of Pathology, Kazan State Medical University, 420012 Kazan, Russia; (K.S.); (F.B.); (A.G.)
| | - Aigul Galembikova
- Department of Pathology, Kazan State Medical University, 420012 Kazan, Russia; (K.S.); (F.B.); (A.G.)
| | - Svetlana Zykova
- Department of Pharmacology, Perm State Academy of Pharmacy, 614990 Perm, Russia; (S.Z.); (K.G.); (S.I.); (N.I.)
| | - Ksenia Gankova
- Department of Pharmacology, Perm State Academy of Pharmacy, 614990 Perm, Russia; (S.Z.); (K.G.); (S.I.); (N.I.)
| | - Sergei Igidov
- Department of Pharmacology, Perm State Academy of Pharmacy, 614990 Perm, Russia; (S.Z.); (K.G.); (S.I.); (N.I.)
| | - Nazim Igidov
- Department of Pharmacology, Perm State Academy of Pharmacy, 614990 Perm, Russia; (S.Z.); (K.G.); (S.I.); (N.I.)
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48
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Computational-Based Discovery of the Anti-Cancer Activities of Pyrrole-Based Compounds Targeting the Colchicine-Binding Site of Tubulin. Molecules 2022. [PMID: 35566235 DOI: 10.3390/molecules27092873.(] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
Despite the tubulin-binding agents (TBAs) that are widely used in the clinic for cancer therapy, tumor resistance to TBAs (both inherited and acquired) significantly impairs their effectiveness, thereby decreasing overall survival (OS) and progression-free survival (PFS) rates, especially for the patients with metastatic, recurrent, and unresectable forms of the disease. Therefore, the development of novel effective drugs interfering with the microtubules' dynamic state remains a big challenge in current oncology. We report here about the novel ethyl 2-amino-1-(furan-2-carboxamido)-5-(2-aryl/tert-butyl-2-oxoethylidene)-4-oxo-4,5-dihydro-1H-pyrrole-3-carboxylates (EAPCs) exhibiting potent anti-cancer activities against the breast and lung cancer cell lines in vitro. This was due to their ability to inhibit tubulin polymerization and induce cell cycle arrest in M-phase. As an outcome, the EAPC-treated cancer cells exhibited a significant increase in apoptosis, which was evidenced by the expression of cleaved forms of PARP, caspase-3, and increased numbers of Annexin-V-positive cells. By using the in silico molecular modeling methods (e.g., induced-fit docking, binding metadynamics, and unbiased molecular dynamics), we found that EAPC-67 and -70 preferentially bind to the colchicine-binding site of tubulin. Lastly, we have shown that the EAPCs indicated above and colchicine utilizes a similar molecular mechanism to inhibit tubulin polymerization via targeting the T7 loop in the β-chain of tubulin, thereby preventing the conformational changes in the tubulin dimers required for their polymerization. Collectively, we identified the novel and potent TBAs that bind to the colchicine-binding site and disrupt the microtubule network. As a result of these events, the compounds induced a robust cell cycle arrest in M-phase and exhibited potent pro-apoptotic activities against the epithelial cancer cell lines in vitro.
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49
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Agoni C, Salifu EY, Enslin G, Kwofie SK, Soliman ME. Dual-Inhibition of Human N-Myristoyltransferase Subtypes Halts Common Cold Pathogenesis: Atomistic Perspectives from the Case of IMP-1088. Chem Biodivers 2022; 19:e202100748. [PMID: 34936193 DOI: 10.1002/cbdv.202100748] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 12/21/2021] [Indexed: 12/31/2022]
Abstract
The pharmacological inhibition of human N-myristoyltransferase (HsNMT) has emerged as an efficient strategy to completely prevent the replication process of rhinoviruses, a potential treatment for the common cold. This was corroborated by the recent discovery of compound IMP-1088, a novel inhibitor that demonstrated a dual-inhibitory activity against the two HsNMT subtypes 1 and 2 without inducing cytotoxicity. However, the molecular and structural basis for the dual-inhibitory potential of IMP-1088 has not been investigated. As such, we employ molecular modelling techniques to resolve the structural mechanisms that account for the dual-inhibitory prowess of IMP-1088. Sequence and nanosecond-based analyses identified Tyr296, Phe190, Tyr420, Leu453, Gln496, Val181, Leu474, Glu182, and Asn246 as residues common within the binding pockets of both HsNMT1 and HsNMT2 subtypes whose consistent interactions with IMP-1088 underpin the basis for its dual inhibitory potency. Nano-second-based assessment of interaction dynamics revealed that Tyr296 consistently elicited high-affinity π-π stacked interaction with IMP-1088, thus further highlighting its cruciality corroborating previous report. An exploration of resulting structural changes upon IMP-1088 binding further revealed a characteristic impeding of residue fluctuations, structural compactness, and a consequential burial of crucial hydrophobic residues, features required for HsNMT1/2 functionality. Findings present essential structural perspectives that augment previous experimental efforts and could also advance drug development for treating respiratory tract infections, especially those mediated by rhinoviruses.
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Affiliation(s)
- Clement Agoni
- Department of Pharmaceutical Sciences, Tshwane University of Technology, Arcadia Campus, Pretoria, South Africa
| | - Elliasu Y Salifu
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Gill Enslin
- Department of Pharmaceutical Sciences, Tshwane University of Technology, Arcadia Campus, Pretoria, South Africa
| | - Samuel K Kwofie
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic & Applied Sciences, University of Ghana, PMB LG 77, Legon, Accra, Ghana.,West African Center for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Mahmoud E Soliman
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
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50
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Dhorma LP, Teli MK, Nangunuri BG, Venkanna A, Ragam R, Maturi A, Mirzaei A, Vo DK, Maeng HJ, Kim MH. Positioning of an unprecedented 1,5-oxaza spiroquinone scaffold into SMYD2 inhibitors in epigenetic space. Eur J Med Chem 2022; 227:113880. [PMID: 34656041 DOI: 10.1016/j.ejmech.2021.113880] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 09/04/2021] [Accepted: 09/28/2021] [Indexed: 11/26/2022]
Abstract
Lysine methyltransferases are important regulators of epigenetic signaling and are emerging as a novel drug target for drug discovery. This work demonstrates the positioning of novel 1,5-oxaza spiroquinone scaffold into selective SET and MYND domain-containing proteins 2 methyltransferases inhibitors. Selectivity of the scaffold was identified by epigenetic target screening followed by SAR study for the scaffold. The optimization was performed iteratively by two-step optimization consisting of iterative synthesis and computational studies (docking, metadynamics simulations). Computational binding studies guided the important interactions of the spiro[5.5]undeca scaffold in pocket 1 and Lysine channel and suggested extension of tail length for the improvement of potency (IC50: up to 399 nM). The effective performance of cell proliferation assay for chosen compounds (IC50: up to 11.9 nM) led to further evaluation in xenograft assay. The potent compound 24 demonstrated desirable in vivo efficacy with growth inhibition rate of 77.7% (4 fold decrease of tumor weight and 3 fold decrease of tumor volume). Moreover, mirosomal assay and pharmacokinetic profile suggested further developability of this scaffold through the identification of major metabolites (dealkylation at silyl group, reversible hydration product, the absence of toxic quinone fragments) and enough exposure of the testing compound 24 in plasma. Such spiro[5.5]undeca framework or ring system was neither been reported nor suggested as a modulator of methyltransferases. The chemo-centric target positioning and structural novelty can lead to potential pharmacological benefit.
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Affiliation(s)
- Lama Prema Dhorma
- Department of Pharmacy and Gachon Institute of Pharmaceutical Science, College of Pharmacy, Gachon University, Yeonsu-gu, Incheon, South Korea
| | - Mahesh K Teli
- Department of Pharmacy and Gachon Institute of Pharmaceutical Science, College of Pharmacy, Gachon University, Yeonsu-gu, Incheon, South Korea
| | - Bhargav Gupta Nangunuri
- Department of Pharmacy and Gachon Institute of Pharmaceutical Science, College of Pharmacy, Gachon University, Yeonsu-gu, Incheon, South Korea
| | - Arramshetti Venkanna
- Department of Pharmacy and Gachon Institute of Pharmaceutical Science, College of Pharmacy, Gachon University, Yeonsu-gu, Incheon, South Korea
| | - Rao Ragam
- Department of Pharmacy and Gachon Institute of Pharmaceutical Science, College of Pharmacy, Gachon University, Yeonsu-gu, Incheon, South Korea
| | - Arunkranthi Maturi
- Department of Pharmacy and Gachon Institute of Pharmaceutical Science, College of Pharmacy, Gachon University, Yeonsu-gu, Incheon, South Korea
| | - Anvar Mirzaei
- Department of Pharmacy and Gachon Institute of Pharmaceutical Science, College of Pharmacy, Gachon University, Yeonsu-gu, Incheon, South Korea
| | - Dang-Khoa Vo
- Department of Pharmacy and Gachon Institute of Pharmaceutical Science, College of Pharmacy, Gachon University, Yeonsu-gu, Incheon, South Korea
| | - Han-Joo Maeng
- Department of Pharmacy and Gachon Institute of Pharmaceutical Science, College of Pharmacy, Gachon University, Yeonsu-gu, Incheon, South Korea
| | - Mi-Hyun Kim
- Department of Pharmacy and Gachon Institute of Pharmaceutical Science, College of Pharmacy, Gachon University, Yeonsu-gu, Incheon, South Korea.
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