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Yu Y, Hu Y, Yan H, Zeng X, Yang H, Xu L, Sheng R. Discovery of 5-(1-benzyl-1H-imidazol-4-yl)-1,2,4-oxadiazole derivatives as novel RIPK1 inhibitors via structure-based virtual screening. Drug Dev Res 2024; 85:e22235. [PMID: 39021343 DOI: 10.1002/ddr.22235] [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: 04/13/2024] [Revised: 06/05/2024] [Accepted: 06/26/2024] [Indexed: 07/20/2024]
Abstract
RIPK1 plays a key role in necroptosis and is associated with various inflammatory diseases. Using structure-based virtual screening, a novel hit with 5-(1-benzyl-1H-imidazol-4-yl)-1,2,4-oxadiazole scaffold was identified as an RIPK1 inhibitor with an IC50 value of 1.3 μM. Further structure-activity relationship study was performed based on similarity research and biological evaluation. The molecular dynamics simulation of compound 2 with RIPK1 indicated that it may act as a type II kinase inhibitor. This study provides a highly efficient way to discover novel scaffold RIPK1 inhibitors for further development.
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Affiliation(s)
- Yanzhen Yu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Yunzhen Hu
- Department of Clinical Pharmacy, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Huihui Yan
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Xin Zeng
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Haodong Yang
- Jinhua Institute of Zhejiang University, Zhejiang University, Jinhua, China
| | - Lei Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
| | - Rong Sheng
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
- Jinhua Institute of Zhejiang University, Zhejiang University, Jinhua, China
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2
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Ahamad S, Junaid IT, Gupta D. Computational Design of Novel Tau-Tubulin Kinase 1 Inhibitors for Neurodegenerative Diseases. Pharmaceuticals (Basel) 2024; 17:952. [PMID: 39065802 PMCID: PMC11280166 DOI: 10.3390/ph17070952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 06/14/2024] [Accepted: 06/20/2024] [Indexed: 07/28/2024] Open
Abstract
The tau-tubulin kinase 1 (TTBK1) protein is a casein kinase 1 superfamily member located at chromosome 6p21.1. It is expressed explicitly in the brain, particularly in the cytoplasm of cortical and hippocampal neurons. TTBK1 has been implicated in the phosphorylation and aggregation of tau in Alzheimer's disease (AD). Considering its significance in AD, TTBK1 has emerged as a promising target for AD treatment. In the present study, we identified novel TTBK1 inhibitors using various computational techniques. We performed a virtual screening-based docking study followed by E-pharmacophore modeling, cavity-based pharmacophore, and ligand design techniques and found ZINC000095101333, LD7, LD55, and LD75 to be potential novel TTBK1 lead inhibitors. The docking results were complemented by Molecular Mechanics/Generalized Born Surface Area (MMGBSA) calculations. The molecular dynamics (MD) simulation studies at a 500 ns scale were carried out to monitor the behavior of the protein toward the identified ligands. Pharmacological and ADME/T studies were carried out to check the drug-likeness of the compounds. In summary, we identified a new series of compounds that could effectively bind the TTBK1 receptor. The newly designed compounds are promising candidates for developing therapeutics targeting TTBK1 for AD.
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Affiliation(s)
- Shahzaib Ahamad
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Iqbal Taliy Junaid
- Malaria Biology, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India;
| | - Dinesh Gupta
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
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3
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Abdel-Naim AB, Kumar P, Bazuhair MA, Rizg WY, Niyazi HA, Alkuwaity K, Niyazi HA, Alharthy SA, Harakeh S, Haque S, Prakash A, Kumar V. Computational insights into dynamics and conformational stability of N-acetylmannosamine kinase mutations. J Biomol Struct Dyn 2024:1-11. [PMID: 38502682 DOI: 10.1080/07391102.2024.2323702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 02/21/2024] [Indexed: 03/21/2024]
Abstract
The activity of UDP-GlcNAc 2-epimerase/ManNAc kinase (GNE) is essential for the biosynthesis of sialic acid, which is involved in cellular processes in health and diseases. GNE contains an N-terminal epimerase domain and a C-terminal kinase domain (N-acetylmannosamine kinase, MNK). Mutations of the GNE protein led to hypoactivity of the enzyme and cause sialurea or autosomal recessive inclusion body myopathy/Nonaka myopathy. Here, we used all-atom molecular dynamics (MD) simulations to comprehend the folding, dynamics and conformational stability of MNK variants, including the wild type (WT) and three mutants (H677R, V696M and H677R/V696M). The deleterious and destabilizing nature of MNK mutants were predicted using different prediction tools. Results predicted that mutations modulate the stability, flexibility and function of MNK. The effect of mutations on the conformational stability and dynamics of MNK was next studied through the free-energy landscape (FEL), hydrogen-bonds and secondary structure changes. The FEL results show that the mutations interfere with various conformational transitions in both WT and mutants, exposing the structural underpinnings of protein destabilization and unfolding brought on by mutation. We discover that, when compared to the other two mutations, V696M and H677R/V696M, H677R has the most harmful effects. These findings have a strong correlation with published experimental studies that demonstrate how these mutations disrupt MNK activity. Hence, this computational study describes the structural details to unravel the mutant effects at the atomistic resolution and has implications for understanding the GNE's physiological and pathological role.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ashraf B Abdel-Naim
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
- Mohamed Saeed Tamer Chair for Pharmaceutical Industries, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
- Center of Excellence for Drug Research and Pharmaceutical Industries, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Pawan Kumar
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Mohammed A Bazuhair
- Center of Excellence for Drug Research and Pharmaceutical Industries, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Clinical Pharmacology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Waleed Y Rizg
- Mohamed Saeed Tamer Chair for Pharmaceutical Industries, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
- Center of Excellence for Drug Research and Pharmaceutical Industries, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Pharmaceutics, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hatoon A Niyazi
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Khalil Alkuwaity
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hanouf A Niyazi
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Saif A Alharthy
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Toxicology and Forensic Sciences Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Steve Harakeh
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Yousef Abdul Latif Jameel Scientific Chair of Prophetic Medicine Application, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Health Sciences, Jazan University, Jazan, Saudi Arabia
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, Lebanon
- Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates
| | - Amresh Prakash
- Amity Institute of Integrative Sciences and Health, Amity University Haryana, Gurgaon, India
| | - Vijay Kumar
- Amity Institute of Neuropsychology & Neurosciences, Amity University, Noida, India
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4
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Rymbai E, Roy D, Jupudi S, Srinivasadesikan V. The identification of c-Abl inhibitors as potential agents for Parkinson's disease: a preliminary in silico approach. Mol Divers 2024:10.1007/s11030-023-10796-3. [PMID: 38273156 DOI: 10.1007/s11030-023-10796-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 12/18/2023] [Indexed: 01/27/2024]
Abstract
Parkinson's disease (PD) is the most common movement disorder worldwide. PD is primarily associated with the mutation, overexpression, and phosphorylation of α-synuclein. At the molecular level, the upstream protein c-Abl, a tyrosine kinase, has been shown to regulate α-synuclein activation and expression patterns. This study aimed to identify potential c-Abl inhibitors through in silico approaches. Molecular docking was performed using PyRx software, followed by Prime MM-GBSA studies. BBB permeability and toxicity were predicted using CBligand and ProTox-II, respectively. ADME was assessed using QikProp. Molecular dynamics were carried out using Desmond (Academic version). DFT calculations were performed using the Gaussian 16 suite program. The binding scores of the top hits, norimatinib, DB07326, and entinostat were - 11.8 kcal/mol, - 11.8 kcal/mol, and - 10.8 kcal/mol, respectively. These hits displayed drug-likeness with acceptable ADME properties, except for the standard, nilotinib, which violated Lipinski's rule of five. Similarly, the molecular dynamics showed that the top hits remained stable during the 100 ns simulation. DFT results indicate DB04739 as a potent reactive hit. While based on toxicity prediction, entinostat may be a potential candidate for preclinical and clinical testing in PD. Further studies are warranted to confirm the activity and efficacy of these ligands for PD.
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Affiliation(s)
- Emdormi Rymbai
- Department of Pharmacology, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty, Nilgiris, Tamil Nadu, India.
| | - Dhritiman Roy
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh, Assam, India
| | - Srikanth Jupudi
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty, Nilgiris, Tamil Nadu, India
| | - Venkatesan Srinivasadesikan
- Department of Sciences and Humanities, Vignan's Foundation for Science, Technology and Research (Deemed to be University), Vadlamudi, Guntur, Andhra Pradesh, India
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5
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Siddiqui NF, Vishwakarma P, Thakur S, Jadhav HR. Bioactivity predictions and virtual screening using machine learning predictive model. J Biomol Struct Dyn 2024:1-20. [PMID: 38217308 DOI: 10.1080/07391102.2023.2300132] [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: 09/20/2023] [Accepted: 12/23/2023] [Indexed: 01/15/2024]
Abstract
Recently, there has been significant attention on machine learning algorithms for predictive modeling. Prediction models for enzyme inhibitors are limited, and it is essential to account for chemical biases while developing them. The lack of repeatability in available models and chemical bias issues constrain drug discovery and development. A new prediction model for enzyme inhibitors has been developed, and the model efficacy was checked using Dipeptidyl peptidase 4 (DPP-4) inhibitors. A Python script was prepared and can be provided for personal use upon request. Among various machine learning algorithms, it was found that Random Forest offers the best accuracy. Two models were compared, one with diverse training and test data and the other with a random split. It was concluded that machine learning predictive models based on the Murcko scaffold can address chemical bias concerns. In-silico screening of the Drug Bank database identified two molecules against DPP-4, which are previously proven hit molecules. The approach was further validated through molecular docking studies and molecular dynamics simulations, demonstrating the credibility and relevance of the developed model for future investigations and potential translation into clinical applications.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Noor Fatima Siddiqui
- Department of Pharmacy, Pharmaceutical Chemistry Research Laboratory, Birla Institute of Technology and Science Pilani, Pilani, RJ, India
| | - Pinky Vishwakarma
- Department of Pharmacy, Pharmaceutical Chemistry Research Laboratory, Birla Institute of Technology and Science Pilani, Pilani, RJ, India
| | - Shikha Thakur
- Department of Pharmacy, Pharmaceutical Chemistry Research Laboratory, Birla Institute of Technology and Science Pilani, Pilani, RJ, India
| | - Hemant R Jadhav
- Department of Pharmacy, Pharmaceutical Chemistry Research Laboratory, Birla Institute of Technology and Science Pilani, Pilani, RJ, India
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Zhou M, Ma X, Gao M, Wu H, Liu Y, Shi X, Dai M. Paeonol Attenuates Atherosclerosis by Inhibiting Vascular Smooth Muscle Cells Senescence via SIRT1/P53/TRF2 Signaling Pathway. Molecules 2024; 29:261. [PMID: 38202844 PMCID: PMC10780795 DOI: 10.3390/molecules29010261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/28/2023] [Accepted: 01/02/2024] [Indexed: 01/12/2024] Open
Abstract
Atherosclerosis is a chronic inflammatory disease leading to various vascular diseases. Vascular smooth muscle cell (VSMC) senescence promotes atherosclerotic inflammation and the formation of plaque necrosis core, in part through telomere damage mediated by a high-fat diet. Our previous research found that paeonol, a potential anti-inflammatory agent extracted from Cortex Moutan, could significantly improve VSMCs dysfunction. However, the impact of paeonol on the senescence of VSMCs remains unexplored. This study presents the protective effects of paeonol on VSMCs senescence, and its potential activity in inhibiting the progression of atherosclerosis in vivo and in vitro. Sirtuin 1 (SIRT1) is a nuclear deacetylase involved in cell proliferation, senescence, telomere damage, and inflammation. Here, SIRT1 was identified as a potential target of paeonol having anti-senescence and anti-atherosclerosis activity. Mechanistic studies revealed that paeonol binds directly to SIRT1 and then activates the SIRT1/P53/TRF2 pathway to inhibit VSMCs senescence. Our results suggested that SIRT1-mediated VSMCs senescence is a promising druggable target for atherosclerosis, and that pharmacological modulation of the SIRT1/P53/TRF2 signaling pathway by paeonol is of potential benefit for patients with atherosclerosis.
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Affiliation(s)
- Min Zhou
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China; (M.Z.); (X.M.); (M.G.); (H.W.); (Y.L.)
| | - Xiaolin Ma
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China; (M.Z.); (X.M.); (M.G.); (H.W.); (Y.L.)
| | - Menglong Gao
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China; (M.Z.); (X.M.); (M.G.); (H.W.); (Y.L.)
| | - Hongfei Wu
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China; (M.Z.); (X.M.); (M.G.); (H.W.); (Y.L.)
- Anhui Key Laboratory for Research and Development of Traditional Chinese Medicine, Hefei 230012, China
| | - Yarong Liu
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China; (M.Z.); (X.M.); (M.G.); (H.W.); (Y.L.)
- Anhui Key Laboratory for Research and Development of Traditional Chinese Medicine, Hefei 230012, China
| | - Xiaoyan Shi
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China; (M.Z.); (X.M.); (M.G.); (H.W.); (Y.L.)
| | - Min Dai
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China; (M.Z.); (X.M.); (M.G.); (H.W.); (Y.L.)
- Anhui Key Laboratory for Research and Development of Traditional Chinese Medicine, Hefei 230012, China
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7
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Ahamad S, Hema K, Gupta D. Identification of Novel Tau-Tubulin Kinase 2 Inhibitors Using Computational Approaches. ACS OMEGA 2023; 8:13026-13037. [PMID: 37065061 PMCID: PMC10099139 DOI: 10.1021/acsomega.3c00225] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 02/09/2023] [Indexed: 06/19/2023]
Abstract
Tau tubulin kinase 2 (TTBK2) associated with multiple diseases is one of the kinases which phosphorylates tau and tubulin. Numerous efforts have been made to understand the role of TTBK2 in protein folding mechanisms and misfolding behavior. The misfolded protein intermediates form polymers with unwanted aggregation properties that initiate several diseases, including Alzheimer's. The availability of TTBK2 inhibitors can enhance the understanding of the molecular mechanism of action of the kinase and assist in developing novel therapeutics. In the quest for TTBK2 inhibitors, this study focuses on screening two chemical libraries (ChEMBL and ZINC-FDA). The molecular docking, RO5/absorption, distribution, metabolism, and excretion/toxicity, density functional theory, molecular dynamics (MD) simulations, and molecular mechanics with generalized Born and surface area solvation techniques enabled shortlisting of the four most active compounds, namely, ChEMBL1236395, ChEMBL2104398, ChEMBL3427435, and ZINC000000509440. Moreover, 500 ns MD simulation was performed for each complex, which provided valuable insights into the structural changes in the complexes. The relative fluctuation, solvent accessible surface area, atomic gyration, compactness covariance, and free energy landscapes revealed that the compounds could stabilize the TTBK2 protein. Overall, this study would be valuable for the researchers targeting the development of novel TTBK2 inhibitors.
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Khazamipour A, Gholampour-Faroji N, Zeraati T, Vakilian F, Haddad-Mashadrizeh A, Ghayour Mobarhan M, Pasdar A. A novel causative functional mutation in GATA6 gene is responsible for familial dilated cardiomyopathy as supported by in silico functional analysis. Sci Rep 2022; 12:13752. [PMID: 35962153 PMCID: PMC9374661 DOI: 10.1038/s41598-022-13993-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 05/31/2022] [Indexed: 11/09/2022] Open
Abstract
Dilated cardiomyopathy (DCM), one of the most common types of cardiomyopathies has a heterogeneous nature and can be seen in Mendelian forms. Next Generation Sequencing is a powerful tool for identifying novel variants in monogenic disorders. We used whole-exome sequencing (WES) and Sanger sequencing techniques to identify the causative mutation of DCM in an Iranian pedigree. We found a novel variant in the GATA6 gene, leading to substituting Histidine by Tyrosine at position 329, observed in all affected family members in the pedigree, whereas it was not established in any of the unaffected ones. We hypothesized that the H329Y mutation may be causative for the familial pattern of DCM in this family. The predicted models of GATA6 and H329Y showed the high quality according to PROCHECK and ERRAT. Nonetheless, simulation results revealed that the protein stability decreased after mutation, while the flexibility may have been increased. Hence, the mutation led to the increased compactness of GATA6. Overall, these data indicated that the mutation could affect the protein structure, which may be related to the functional impairment of GATA6 upon H329Y mutation, likewise their involvement in pathologies. Further functional investigations would help elucidating the exact mechanism.
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Affiliation(s)
- Afrouz Khazamipour
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Nazanin Gholampour-Faroji
- Biotechnology Department, Iranian Research Organization for Science and Technology (IROST), Tehran, Iran
| | - Tina Zeraati
- Medical Genetics Research Centre, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Farveh Vakilian
- Atherosclerosis Prevention Research Centre, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Aliakbar Haddad-Mashadrizeh
- Industrial Biotechnology Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Majid Ghayour Mobarhan
- Metabolic Syndrome Research Centre, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Alireza Pasdar
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran. .,Medical Genetics Research Centre, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran. .,Division of Applied Medicine, Medical School, University of Aberdeen, Foresterhill, Aberdeen, UK. .,Bioinformatics Research Centre, Mashhad University of Medical Sciences, Mashhad, Iran.
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9
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Almeleebia TM, Ahamad S, Ahmad I, Alshehri A, Alkhathami AG, Alshahrani MY, Asiri MA, Saeed A, Siddiqui JA, Yadav DK, Saeed M. Identification of PARP12 Inhibitors By Virtual Screening and Molecular Dynamics Simulations. Front Pharmacol 2022; 13:847499. [PMID: 36016564 PMCID: PMC9395932 DOI: 10.3389/fphar.2022.847499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Accepted: 04/27/2022] [Indexed: 11/13/2022] Open
Abstract
Poly [adenosine diphosphate (ADP)-ribose] polymerases (PARPs) are members of a family of 17 enzymes that performs several fundamental cellular processes. Aberrant activity (mutation) in PARP12 has been linked to various diseases including inflammation, cardiovascular disease, and cancer. Herein, a large library of compounds (ZINC-FDA database) has been screened virtually to identify potential PARP12 inhibitor(s). The best compounds were selected on the basis of binding affinity scores and poses. Molecular dynamics (MD) simulation and binding free energy calculation (MMGBSA) were carried out to delineate the stability and dynamics of the resulting complexes. To this end, root means deviations, relative fluctuation, atomic gyration, compactness, covariance, residue-residue contact map, and free energy landscapes were studied. These studies have revealed that compounds ZINC03830332, ZINC03830554, and ZINC03831186 are promising agents against mutated PARP12.
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Affiliation(s)
- Tahani M. Almeleebia
- Department of Clinical Pharmacy, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | | | - Irfan Ahmad
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Ahmad Alshehri
- College of Applied Medical Sciences, Najran University, Najran, Saudi Arabia
| | - Ali G. Alkhathami
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Mohammad Y. Alshahrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Mohammed A. Asiri
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Amir Saeed
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail, Saudi Arabia
- Department of Medical Microbiology, Faculty of Medical Laboratory Sciences, University of Medical Sciences and Technology, Khartoum, Sudan
| | - Jamshaid Ahmad Siddiqui
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, India
| | - Dharmendra K. Yadav
- Department of Pharmacy, Gachon Institute of Pharmaceutical Sciences, College of Pharmacy, Gachon University of Medicine and Science, Incheon, South Korea
- *Correspondence: Mohd Saeed, ; Dharmendra K. Yadav,
| | - Mohd Saeed
- Department of Biology, College of Sciences, University of Hail, Hail, Saudi Arabia
- *Correspondence: Mohd Saeed, ; Dharmendra K. Yadav,
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10
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Santos JL, Janegitz BC, de Oliveira MR, de Souza GL. Exploring the water hydrogen-bonding effects on the ground and low-lying excited states of serotonin. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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11
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Wang L, Ding MY, Wang J, Gao JG, Liu RM, Li HT. Effects of Site-Directed Mutagenesis of Cysteine on the Structure of Sip Proteins. Front Microbiol 2022; 13:805325. [PMID: 35572629 PMCID: PMC9100928 DOI: 10.3389/fmicb.2022.805325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 02/22/2022] [Indexed: 11/16/2022] Open
Abstract
Bacillus thuringiensis, a gram-positive bacteria, has three insecticidal proteins: Vip (vegetative insecticidal protein), Cry (crystal), and Sip (secreted insecticidal protein). Of the three, Sip proteins have insecticidal activity against larvae of Coleoptera. However, the Sip1Aa protein has little solubility in the supernatant because of inclusion bodies. This makes it more difficult to study, and thus research on Sip proteins is limited, which hinders the study of their mechanistic functions and insecticidal mechanisms. This highlights the importance of further investigation of the Sip1Aa protein. Disulfide bonds play an important role in the stability and function of proteins. Here, we successfully constructed mutant proteins with high insecticidal activity. The tertiary structure of the Sip1Aa protein was analyzed with homologous modeling and bioinformatics to predict the conserved domain of the protein. Cysteine was used to replace amino acids via site-directed mutagenesis. We successfully constructed Sip149-251, Sip153-248, Sip158-243, and Sip178-314 mutant proteins with higher solubility than Sip1Aa. Sip153-248 and Sip158-243 were the most stable compared to Sip1Aa, followed by Sip149-251 and Sip178-314. The insecticidal activity of Sip153-248 (Sip158-243) was 2.76 (2.26) times higher than that of Sip1Aa. The insecticidal activity of Sip149-251 and Sip178-314 did not differ significantly from that of Sip1Aa. Basic structural properties, physicochemical properties, and the spatial structure of the mutation site of Sip1Aa and the mutant proteins were analyzed. These results provide a molecular basis for using Sip1Aa to control Coleopteran insects and contribute to the study of the Sip1Aa insecticidal mechanism.
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Affiliation(s)
- Lin Wang
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Ming-Yue Ding
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Jing Wang
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Ji-Guo Gao
- College of Life Science, Northeast Agricultural University, Harbin, China
- *Correspondence: Ji-Guo Gao,
| | - Rong-Mei Liu
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Hai-Tao Li
- College of Life Science, Northeast Agricultural University, Harbin, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Hai-Tao Li,
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