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Kumar S U, Varghese RP, Preethi VA, Doss CGP, Zayed H. Identification of Potential Inhibitors Targeting GTPase-Kirsten RAt Sarcoma Virus (K-Ras) Driven Cancers via E-Pharmacophore-Based Virtual Screening and Drug Repurposing Approach. FRONT BIOSCI-LANDMRK 2023; 28:288. [PMID: 38062837 DOI: 10.31083/j.fbl2811288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 06/08/2023] [Accepted: 09/11/2023] [Indexed: 12/18/2023]
Abstract
BACKGROUND Mutations in the K-Ras gene are among the most frequent genetic alterations in various cancers, and inhibiting RAS signaling has shown promising results in treating solid tumors. However, finding effective drugs that can bind to the RAS protein remains challenging. This drove us to explore new compounds that could inhibit tumor growth, particularly in cancers that harbor K-Ras mutations. METHODS Our study used bioinformatic techniques such as E-pharmacophore virtual screening, molecular simulation, principal component analysis (PCA), extra precision (XP) docking, and ADMET analyses to identify potential inhibitors for K-Ras mutants G12C and G12D. RESULTS In our study, we discovered that inhibitors such as afatinib, osimertinib, and hydroxychloroquine strongly inhibit the G12C mutant. Similarly, hydroxyzine, zuclopenthixol, fluphenazine, and doxapram were potent inhibitors for the G12D mutant. Notably, all six of these molecules exhibit a high binding affinity for the H95 cryptic groove present in the mutant structure. These molecules exhibited a unique affinity mechanism at the molecular level, which was further enhanced by hydrophobic interactions. Molecular simulations and PCA revealed the formation of stable complexes within switch regions I and II. This was particularly evident in three complexes: G12C-osimertinib, G12D-fluphenazine, and G12D-zuclopenthixol. Despite the dynamic nature of switches I and II in K-Ras, the interaction of inhibitors remained stable. According to QikProp results, the properties and descriptors of the selected molecules fell within an acceptable range compared to sotorasib. CONCLUSIONS We have successfully identified potential inhibitors of the K-Ras protein, laying the groundwork for the development of targeted therapies for cancers driven by K-Ras mutations.
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Affiliation(s)
- Udhaya Kumar S
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, 632014 Vellore, Tamil Nadu, India
| | - Rinku Polachirakkal Varghese
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, 632014 Vellore, Tamil Nadu, India
| | - V Anu Preethi
- School of Computer Science and Engineering, Vellore Institute of Technology, 632014 Vellore, Tamil Nadu, India
| | - C George Priya Doss
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, 632014 Vellore, Tamil Nadu, India
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health and Sciences, Qatar University, 2713 QU Health, Doha, Qatar
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Shavlokhova V, Vollmer A, Zouboulis CC, Vollmer M, Wollborn J, Lang G, Kübler A, Hartmann S, Stoll C, Roider E, Saravi B. Finetuning of GLIDE stable diffusion model for AI-based text-conditional image synthesis of dermoscopic images. Front Med (Lausanne) 2023; 10:1231436. [PMID: 37928464 PMCID: PMC10623307 DOI: 10.3389/fmed.2023.1231436] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 10/09/2023] [Indexed: 11/07/2023] Open
Abstract
Background The development of artificial intelligence (AI)-based algorithms and advances in medical domains rely on large datasets. A recent advancement in text-to-image generative AI is GLIDE (Guided Language to Image Diffusion for Generation and Editing). There are a number of representations available in the GLIDE model, but it has not been refined for medical applications. Methods For text-conditional image synthesis with classifier-free guidance, we have fine-tuned GLIDE using 10,015 dermoscopic images of seven diagnostic entities, including melanoma and melanocytic nevi. Photorealistic synthetic samples of each diagnostic entity were created by the algorithm. Following this, an experienced dermatologist reviewed 140 images (20 of each entity), with 10 samples originating from artificial intelligence and 10 from original images from the dataset. The dermatologist classified the provided images according to the seven diagnostic entities. Additionally, the dermatologist was asked to indicate whether or not a particular image was created by AI. Further, we trained a deep learning model to compare the diagnostic results of dermatologist versus machine for entity classification. Results The results indicate that the generated images possess varying degrees of quality and realism, with melanocytic nevi and melanoma having higher similarity to real images than other classes. The integration of synthetic images improved the classification performance of the model, resulting in higher accuracy and precision. The AI assessment showed superior classification performance compared to dermatologist. Conclusion Overall, the results highlight the potential of synthetic images for training and improving AI models in dermatology to overcome data scarcity.
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Affiliation(s)
- Veronika Shavlokhova
- Maxillofacial Surgery University Hospital Ruppin-Fehrbelliner Straße Neuruppin, Neuruppin, Germany
| | - Andreas Vollmer
- Department of Oral and Maxillofacial Plastic Surgery, University Hospital of Würzburg, Würzburg, Germany
| | - Christos C. Zouboulis
- Departments of Dermatology, Venereology, Allergology and Immunology, Staedtisches Klinikum Dessau, Medical School Theodor Fontane and Faculty of Health Sciences Brandenburg, Dessau, Germany
| | - Michael Vollmer
- Department of Oral and Maxillofacial Surgery, Tuebingen University Hospital, Tuebingen, Germany
| | - Jakob Wollborn
- Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Gernot Lang
- Department of Orthopedics and Trauma Surgery, Medical Centre-Albert-Ludwigs-University of Freiburg, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Alexander Kübler
- Department of Oral and Maxillofacial Plastic Surgery, University Hospital of Würzburg, Würzburg, Germany
| | - Stefan Hartmann
- Department of Oral and Maxillofacial Plastic Surgery, University Hospital of Würzburg, Würzburg, Germany
| | - Christian Stoll
- Maxillofacial Surgery University Hospital Ruppin-Fehrbelliner Straße Neuruppin, Neuruppin, Germany
| | - Elisabeth Roider
- Department of Dermatology, University Hospital of Basel, Basel, Switzerland
| | - Babak Saravi
- Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
- Department of Orthopedics and Trauma Surgery, Medical Centre-Albert-Ludwigs-University of Freiburg, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
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Das A, Sharma HK, Lather V, Pandita D, Agarwal P. Structure-based virtual screening for identification of potential CDC20 inhibitors and their therapeutic evaluation in breast cancer. 3 Biotech 2023; 13:141. [PMID: 37124982 PMCID: PMC10133423 DOI: 10.1007/s13205-023-03554-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 04/06/2023] [Indexed: 05/02/2023] Open
Abstract
Cell division cycle 20 (CDC20), a critical partner of anaphase promoting complex (APC/C), is indispensably required for metaphase-to-anaphase transition. CDC20 overexpression in TNBC breast cancer patients has been found to be correlated with poor prognosis, hence, we aimed to target CDC20 for TNBC therapeutics. In silico molecular docking of large-scale chemical libraries (phytochemicals/synthetic drugs) against CDC20 protein structure identified five synthetic drugs and four phytochemicals as potential hits interacting with CDC20 active site. The molecular selection was done based on docking scores, binding interactions, binding energies and MM/GBSA scores. Further, we analysed ADME profiles for all the hits and identified lidocaine, an aminoamide anaesthetic group of synthetic drug, with high drug-likeness properties. We explored the anti-tumorigenic effects of lidocaine on MDA-MB-231 TNBC breast cancer cells, which resulted in increased growth inhibition in dose-dependent manner. The molecular mechanism behind the cell viability defect mediated by lidocaine was found to be induction of G2/M cell cycle arrest and cellular apoptosis. Notably, lidocaine treatment of TNBC cells also resulted in downregulation of CDC20 gene expression. Thus, this study identifies lidocaine as a potential anti-neoplastic agent for TNBC cells emphasizing CDC20 as a suitable therapeutic target for breast cancer. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03554-7.
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Affiliation(s)
- Amiya Das
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University Uttar Pradesh, Sector 125, Noida, 201313 India
| | - Hitesh Kumar Sharma
- Amity Institute of Pharmacy, Amity University Uttar Pradesh, Sector 125, Noida, 201313 India
| | - Viney Lather
- Amity Institute of Pharmacy, Amity University Uttar Pradesh, Sector 125, Noida, 201313 India
| | - Deepti Pandita
- Department of Pharmaceutics, Delhi Institute of Pharmaceutical Sciences & Research (DIPSAR) Delhi Pharmaceutical Sciences and Research University, Pushp Vihar, Government of NCT of Delhi, New Delhi, 110017 India
- Centre for Advanced Formulation Technology (CAFT), Delhi Pharmaceutical Sciences and Research University, Pushp Vihar, Govt. of NCT of Delhi, New Delhi, 110017 India
| | - Pallavi Agarwal
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University Uttar Pradesh, Sector 125, Noida, 201313 India
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Kumar SU, Priya Doss CG. Computational investigation to identify potent inhibitors of the GTPase-Kirsten RAt sarcoma virus (K-Ras) mutants G12C and G12D. Comput Biol Med 2021; 139:104946. [PMID: 34715554 DOI: 10.1016/j.compbiomed.2021.104946] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 10/12/2021] [Accepted: 10/12/2021] [Indexed: 02/06/2023]
Abstract
K-Ras mutations are frequent in various cancer types, and according to recent research, K-Ras possesses four-drug targeting sites. This increased our interest in finding potential small molecule inhibitors with anticancer activity to treat K-Ras-driven cancers. We utilized integrated bioinformatic strategies, such as XP docking, MM-GBSA, cell-line cytotoxicity prediction, ADMET, and molecular simulation, to discover potential inhibitors of G12C and G12D mutants compared to sotorasib, which is a recent FDA-approved inhibitor of G12C. We identified compounds, such as flupentixol, amlodipine, and fluvoxamine, for the G12C mutant and paroxetine, flupentixol, and zuclopenthixol for the G12D mutant with significant inhibitory functions. All five compounds bound to the H95 cryptic groove of mutant K-Ras with high efficiency and, like sotorasib, retained a novel binding mechanism with additional hydrophobic interactions at the molecular level. Furthermore, the simulation studies suggested that the binding of flupentixol and amlodipine to G12C stabilizes switch I and switch II. In contrast, paroxetine and flupentixol to G12D showed a similar trend compared to sotorasib complexes. Thus, despite the very dynamic functionality of K-Ras switches I and II, the binding of shortlisted compounds is highly stable. Therefore, the reported study provides potential drug candidates for K-Ras inhibition that can be further developed with in vitro and in vivo evidence for targeted therapy.
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Ruiz VG, Czyzyk DJ, Kumar VP, Jorgensen WL, Anderson KS. Targeting the TS dimer interface in bifunctional Cryptosporidium hominis TS-DHFR from parasitic protozoa: Virtual screening identifies novel TS allosteric inhibitors. Bioorg Med Chem Lett 2020; 30:127292. [PMID: 32631514 PMCID: PMC7376443 DOI: 10.1016/j.bmcl.2020.127292] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 05/23/2020] [Accepted: 05/26/2020] [Indexed: 12/20/2022]
Abstract
Effective therapies are lacking to treat gastrointestinal infections caused by the genus Cryptosporidium, which can be fatal in the immunocompromised. One target of interest is Cryptosporidium hominis (C. hominis) thymidylate synthase-dihydrofolate reductase (ChTS-DHFR), a bifunctional enzyme necessary for DNA biosynthesis. Targeting the TS-TS dimer interface is a novel strategy previously used to identify inhibitors against the related bifunctional enzyme in Toxoplasma gondii. In the present study, we target the ChTS dimer interface through homology modeling and high-throughput virtual screening to identifying allosteric, ChTS-specific inhibitors. Our work led to the discovery of methylenedioxyphenyl-aminophenoxypropanol analogues which inhibit ChTS activity in a manner that is both dose-dependent and influenced by the conformation of the enzyme. Preliminary results presented here include an analysis of structure activity relationships and a ChTS-apo crystal structure of ChTS-DHFR supporting the continued development of inhibitors that stabilize a novel pocket formed in the open conformation of ChTS-TS.
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Affiliation(s)
- Victor G Ruiz
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Daniel J Czyzyk
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Vidya P Kumar
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; Department of Chemistry, Yale University, 225 Prospect Street, PO Box 208107, New Haven, CT 06520-8107, USA; Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - William L Jorgensen
- Department of Chemistry, Yale University, 225 Prospect Street, PO Box 208107, New Haven, CT 06520-8107, USA
| | - Karen S Anderson
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA.
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Meenakumari K, Bupesh G, Vasanth S, Vasu C, Pandian K, Prabhu K, Prasath S. Molecular docking based virtual screening of carbonic anhydrase IX with coumarin (a cinnamon compound) derived ligands. Bioinformation 2019; 15:744-749. [PMID: 31831957 PMCID: PMC6900322 DOI: 10.6026/97320630015744] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 10/30/2019] [Accepted: 10/30/2019] [Indexed: 01/22/2023] Open
Abstract
It is of interest to design carbonic anhydrase IX (CAIX) inhibitors with improved features using molecular docking based virtual high through put screening of ligands. Coumarin (a cinnamon compound with pharmacological activity) is known as a potent phytal compound blocking tumor growth. Hence, a series of 17 coumarin derivatives were designed using the CHEMSKETCH software for docking analysis with CAIX. The catalytic site analysis of CAIX for binding with ligand molecules was completed using the SCHRODINGER package (2009). Thus, 17 ligands with optimal binding features with CAIX were selected following the calculation of ADME/T properties. We report ligands #41, #42, #19 and #15 showed good docking score, glide energy and hydrogen bond interactions without vdW clash. We further show that N-(3,4,5-trimethoxy-phenylcarbamoylmethyl) designated as compound #41 have the highest binding energy (-61.58) with optimal interactions with the catalytic residues (THR 199, PRO 201, HIS 119, HIS 94) of CAIX.
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Affiliation(s)
- Krishnamoorthy Meenakumari
- Research and Development Wing, Central Research Laboratory, Sree Balaji Medical College and Hospital (SBMCH), BIHER, Chrompet, Chennai-600044, India
| | - Giridharan Bupesh
- Research and Development Wing, Central Research Laboratory, Sree Balaji Medical College and Hospital (SBMCH), BIHER, Chrompet, Chennai-600044, India
- Department of Virology, King Institute of Preventive Medicine and Research, Guindy, Chennai-600032, India
| | - Shakthivel Vasanth
- Research and Development Wing, Central Research Laboratory, Sree Balaji Medical College and Hospital (SBMCH), BIHER, Chrompet, Chennai-600044, India
| | - C.Arul Vasu
- Department of Zoology, University of Madras, Guindy Campus, Tamil Nadu, India
| | - Kanniyan Pandian
- Department of Inorganic Chemistry, University of Madras, Guindy Campus, Tamil Nadu, India
| | - Kaliyperumal Prabhu
- Department of Anantomy, Sree Balaji Medical College and Hospital, BIHER, Chromepet, Chennai
| | - S Prasath
- Department of Biomedical Engineering, Bharath Institute of Higher Education and Research, Chennai-605005, Tamil Nadu, India
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Cherukupalli S, Chandrasekaran B, Kryštof V, Aleti RR, Sayyad N, Merugu SR, Kushwaha ND, Karpoormath R. Synthesis, anticancer evaluation, and molecular docking studies of some novel 4,6-disubstituted pyrazolo[3,4-d]pyrimidines as cyclin-dependent kinase 2 (CDK2) inhibitors. Bioorg Chem 2018; 79:46-59. [PMID: 29753773 DOI: 10.1016/j.bioorg.2018.02.030] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 02/26/2018] [Accepted: 02/27/2018] [Indexed: 12/22/2022]
Abstract
A novel series of 4,6-disubstituted pyrazolo[3,4-d]pyrimidines (7-43) bearing various anilines at C-4 position and thiophenethyl or thiopentane moieties at C-6 position have been designed and synthesized by molecular hybridization approach. All the synthesized compounds were evaluated for in vitro CDK2/cyclin E and Abl kinase inhibitory activity as well as anti-proliferative activity against K-562 (chronic myelogeneous leukemia), and MCF-7 (breast adenocarcinoma) cell lines. The structure-activity relationship (SAR) studies revealed that compounds with thiophenethyl group at C-6 with mono-substituted anilines at C-4 exhibited better CDK2 inhibitory activity compared to alkyl group (thiopentane) at C-6 and di-substituted anilines at C-4 of the scaffold. In particular, compounds having 2-chloro, 3-nitro and 4-methylthio aniline groups at C-4 displayed significant enzymatic inhibitory activity against CDK2 with single digit micromolar IC50 values. The in silico molecular docking studies suggested possible binding orientation and the binding energies were in agreement with the observed SAR as well as experimental results. In addition, some of the synthesized compounds showed anti-proliferative effects against K-562 and MCF-7 cancer cell lines with IC50 values in a micromolar range. Thus, the synthesized compounds could be considered as new anticancer hits for further lead optimization.
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Affiliation(s)
- Srinivasulu Cherukupalli
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Balakumar Chandrasekaran
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Vladimír Kryštof
- Laboratory of Growth Regulators, Centre of the Region Hana for Biotechnological and Agricultural Research, Palacky University & Institute of Experimental Botany ASCR, Šlechtitelů 27, 78371 Olomouc, Czech Republic
| | - Rajeshwar Reddy Aleti
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Nisar Sayyad
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Srinivas Reddy Merugu
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Narva Deshwar Kushwaha
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Rajshekhar Karpoormath
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa.
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James N, Ramanathan K. Ligand-Based Pharmacophore Screening Strategy: a Pragmatic Approach for Targeting HER Proteins. Appl Biochem Biotechnol 2018; 186:85-108. [PMID: 29508211 DOI: 10.1007/s12010-018-2724-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 02/19/2018] [Indexed: 02/07/2023]
Abstract
Targeting ErbB family of receptors is an important therapeutic option, because of its essential role in the broad spectrum of human cancers, including non-small cell lung cancer (NSCLC). Therefore, in the present work, considerable effort has been made to develop an inhibitor against HER family proteins, by combining the use of pharmacophore modelling, docking scoring functions, and ADME property analysis. Initially, a five-point pharmacophore model was developed using known HER family inhibitors. The generated model was then used as a query to screen a total of 468,880 compounds of three databases namely ZINC, ASINEX, and DrugBank. Subsequently, docking analysis was carried out to obtain hit molecules that could inhibit the HER receptors. Further, analysis of GLIDE scores and ADME properties resulted in one hit namely BAS01025917 with higher glide scores, increased CNS involvement, and good pharmaceutically relevant properties than reference ligand, afatinib. Furthermore, the inhibitory activity of the lead compounds was validated by performing molecular dynamic simulations. Of note, BAS01025917 was found to possess scaffolds with a broad spectrum of antitumor activity. We believe that this novel hit molecule can be further exploited for the development of a pan-HER inhibitor with low toxicity and greater potential.
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Meraj K, Mahto MK, Christina NB, Desai N, Shahbazi S, Bhaskar M. Molecular modeling, docking and ADMET studies towards development of novel Disopyramide analogs for potential inhibition of human voltage gated sodium channel proteins. Bioinformation 2012; 8:1139-46. [PMID: 23275710 PMCID: PMC3530882 DOI: 10.6026/97320630081139] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2012] [Accepted: 09/27/2012] [Indexed: 12/13/2022] Open
Abstract
The sodium "channelopathies" are the first among the ion channel diseases identified and have attracted widespread clinical and scientific interests. Human voltage gated sodium channels are sites of action of several antiarrhythmic drugs, local anesthetics and related antiepileptic drugs. The present study aims to optimize the activity of Disopyramide, by modification in its structures which may improve the drug action by reducing its side effects. Herein, we have selected Human voltage-gated sodium channel protein type 5 as a potent molecular target. Nearly eighty analogs of Disopyramide are designed and optimized. Thirty are selected for energy minimization using Discovery studio and the LigPrep 2.5. Prior to docking, the active sites of all the proteins are identified. The processing, optimization and minimization of all the proteins is done in Protein preparation wizard. The docking study is performed using the GLIDE. Finally top five ranked lead molecules with better dock scores are identified as having strong binding affinity to 2KAV protein than Disopyramide based on XP G scores. These five leads are further docked with other similar voltage gated sodium channel proteins (PDB IDs: 2KBI, 4DCK, 2L53 and 4DJC) and the best scoring analog with each protein is identified. Drug likeliness and comparative bioactivity analysis for all the analogs is done using QikProp 3.4. Results have shown that the top five lead molecules would have the potential to act as better drugs as compared to Disopyramide and would be of interest as promising starting point for designing compounds against various Sodium channelopathies.
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Affiliation(s)
- Khunza Meraj
- Department of Biotechnology, CMR College of Engineering & Technology, Hyderabad, AP, India
| | - Manoj Kumar Mahto
- Department of Biotechnology, Acharya Nagarjuna University, Guntur, AP, India
- Division of Animal Biotechnology, Department of Zoology, Sri Venkateswara University, Tirupati, AP, India
| | - N Blessy Christina
- Department of Human Genetics, Andhra University, Vishakhapatnam, AP, India
| | - Nidhi Desai
- Department of Biotechnology, PESIT, Bangalore University, Bangalore, Karnataka, India
| | - Sajad Shahbazi
- Department of Biotechnology, Kakatiya University, Warangal, AP, India
| | - Matcha Bhaskar
- Division of Animal Biotechnology, Department of Zoology, Sri Venkateswara University, Tirupati, AP, India
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