1
|
Mazumder K, Aktar A, Kerr PG, Dash R, Blanchard CL, Gulzarul Aziz M, Farahnaky A. Insights into seed coats of nine cultivars of Australian lupin: Unravelling LC-QTOF MS-based biochemical profiles, nutritional, functional, antioxidant, and antidiabetic properties together with rationalizing antidiabetic mechanism by in silico approaches. Food Res Int 2024; 195:114970. [PMID: 39277267 DOI: 10.1016/j.foodres.2024.114970] [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: 04/09/2024] [Revised: 08/12/2024] [Accepted: 08/20/2024] [Indexed: 09/17/2024]
Abstract
Lupins, and other legumes, have attained international interest due to their reported remarkable health benefits. Currently, the seed coats are discarded as waste or animal feed. The research presented here summarizes the potential for incorporating the seed coats into 'whole grain' foods. We aimed to identify metabolites found in the seed coats of nine commercial Australian cultivars of lupin (Lupinus angustifolius and L. albus species), and to evaluate and compare their functional, nutritional, antioxidant, and antidiabetic properties, along with in silico exploration of mechanisms of action for selected identified secondary metabolites. The seed coats were found to contain 79 to 90% dietary fibers and substantial quantity of essential macrometals. LC-QTOF MS-based, untargeted bioactive metabolite profiling explored a total of 673 chemical entities, and identified 63 bioactive secondary metabolites including: biophenols, unsaturated fatty acids, triterpenoids, alkaloids, and dietary prebiotics (insoluble fibers). The seed coats from these nine cultivars show substantial antioxidant activity. The cultivars of L. angustifolius inhibit α-amylase and α-glucosidase significantly in vitro. Moreover, in silico docking and dynamic simulation along with ADME/T analysis suggest that quercetin 3-methyl ether and 8-C-methylquercetin 3-methyl ether as molecules, novel in lupin seed coats, are responsible for the α-amylase and α-glucosidase inhibition. The findings indicated that lupin seed coats might be beneficial food components, rather than be discarded as 'mill waste'.
Collapse
Affiliation(s)
- Kishor Mazumder
- Department of Pharmacy, Jashore University of Science and Technology, Jashore, 7408 Jashore, Bangladesh; School of Optometry and Vision Science, UNSW Medicine, University of New South Wales (UNSW), Sydney, NSW, Australia.
| | - Asma Aktar
- Department of Pharmacy, Jashore University of Science and Technology, Jashore, 7408 Jashore, Bangladesh
| | - Philip G Kerr
- School of Dentistry and Medical Sciences, Charles Sturt University, Boorooma St, Wagga Wagga, NSW 2678, Australia
| | - Raju Dash
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju 38066, Republic of Korea
| | - Christopher L Blanchard
- School of Dentistry and Medical Sciences, Charles Sturt University, Boorooma St, Wagga Wagga, NSW 2678, Australia
| | - Mohammad Gulzarul Aziz
- Department of Food Technology and Rural Industries, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Asgar Farahnaky
- Biosciences and Food Technology, School of Science, RMIT University, Melbourne 3083, Australia
| |
Collapse
|
2
|
Cerutti JP, Diniz LA, Santos VC, Vilchez Larrea SC, Alonso GD, Ferreira RS, Dehaen W, Quevedo MA. Structure-Aided Computational Design of Triazole-Based Targeted Covalent Inhibitors of Cruzipain. Molecules 2024; 29:4224. [PMID: 39275072 PMCID: PMC11396839 DOI: 10.3390/molecules29174224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Revised: 08/29/2024] [Accepted: 09/03/2024] [Indexed: 09/16/2024] Open
Abstract
Cruzipain (CZP), the major cysteine protease present in T. cruzi, the ethiological agent of Chagas disease, has attracted particular attention as a therapeutic target for the development of targeted covalent inhibitors (TCI). The vast chemical space associated with the enormous molecular diversity feasible to explore by means of modern synthetic approaches allows the design of CZP inhibitors capable of exhibiting not only an efficient enzyme inhibition but also an adequate translation to anti-T. cruzi activity. In this work, a computer-aided design strategy was developed to combinatorially construct and screen large libraries of 1,4-disubstituted 1,2,3-triazole analogues, further identifying a selected set of candidates for advancement towards synthetic and biological activity evaluation stages. In this way, a virtual molecular library comprising more than 75 thousand diverse and synthetically feasible analogues was studied by means of molecular docking and molecular dynamic simulations in the search of potential TCI of CZP, guiding the synthetic efforts towards a subset of 48 candidates. These were synthesized by applying a Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) centered synthetic scheme, resulting in moderate to good yields and leading to the identification of 12 hits selectively inhibiting CZP activity with IC50 in the low micromolar range. Furthermore, four triazole derivatives showed good anti-T. cruzi inhibition when studied at 50 μM; and Ald-6 excelled for its high antitrypanocidal activity and low cytotoxicity, exhibiting complete in vitro biological activity translation from CZP to T. cruzi. Overall, not only Ald-6 merits further advancement to preclinical in vivo studies, but these findings also shed light on a valuable chemical space where molecular diversity might be explored in the search for efficient triazole-based antichagasic agents.
Collapse
Affiliation(s)
- Juan Pablo Cerutti
- Unidad de Investigación y Desarrollo en Tecnología Farmacéutica (UNITEFA-CONICET), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba (FCQ-UNC), Haya de la Torre y Medina Allende, Córdoba 5000, Argentina
- Sustainable Chemistry for Metals and Molecules, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Lucas Abreu Diniz
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, Belo Horizonte 31270-901, Brazil
| | - Viviane Corrêa Santos
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, Belo Horizonte 31270-901, Brazil
| | - Salomé Catalina Vilchez Larrea
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI-CONICET), Vuelta de Obligado 2490, Ciudad de Buenos Aires 1428, Argentina
| | - Guillermo Daniel Alonso
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI-CONICET), Vuelta de Obligado 2490, Ciudad de Buenos Aires 1428, Argentina
| | - Rafaela Salgado Ferreira
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, Belo Horizonte 31270-901, Brazil
| | - Wim Dehaen
- Sustainable Chemistry for Metals and Molecules, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Mario Alfredo Quevedo
- Unidad de Investigación y Desarrollo en Tecnología Farmacéutica (UNITEFA-CONICET), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba (FCQ-UNC), Haya de la Torre y Medina Allende, Córdoba 5000, Argentina
| |
Collapse
|
3
|
Wang Q, Hu X, Wei Z, Lu H, Liu H. Reinforcement learning-driven exploration of peptide space: accelerating generation of drug-like peptides. Brief Bioinform 2024; 25:bbae444. [PMID: 39256196 PMCID: PMC11387070 DOI: 10.1093/bib/bbae444] [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: 03/17/2024] [Revised: 08/05/2024] [Accepted: 08/27/2024] [Indexed: 09/12/2024] Open
Abstract
Using amino acid residues in peptide generation has solved several key problems, including precise control of amino acid sequence order, customized peptides for property modification, and large-scale peptide synthesis. Proteins contain unknown amino acid residues. Extracting them for the synthesis of drug-like peptides can create novel structures with unique properties, driving drug development. Computer-aided design of novel peptide drug molecules can solve the high-cost and low-efficiency problems in the traditional drug discovery process. Previous studies faced limitations in enhancing the bioactivity and drug-likeness of polypeptide drugs due to less emphasis on the connection relationships in amino acid structures. Thus, we proposed a reinforcement learning-driven generation model based on graph attention mechanisms for peptide generation. By harnessing the advantages of graph attention mechanisms, this model effectively captured the connectivity structures between amino acid residues in peptides. Simultaneously, leveraging reinforcement learning's strength in guiding optimal sequence searches provided a novel approach to peptide design and optimization. This model introduces an actor-critic framework with real-time feedback loops to achieve dynamic balance between attributes, which can customize the generation of multiple peptides for specific targets and enhance the affinity between peptides and targets. Experimental results demonstrate that the generated drug-like peptides meet specified absorption, distribution, metabolism, excretion, and toxicity properties and bioactivity with a success rate of over 90$\%$, thereby significantly accelerating the process of drug-like peptide generation.
Collapse
Affiliation(s)
- Qian Wang
- College of Computer Science and Technology, Ocean University of China, 238 Songling Rd, 266100 Shandong, China
| | - Xiaotong Hu
- College of Computer Science and Technology, Ocean University of China, 238 Songling Rd, 266100 Shandong, China
| | - Zhiqiang Wei
- College of Computer Science and Technology, Ocean University of China, 238 Songling Rd, 266100 Shandong, China
| | - Hao Lu
- College of Computer Science and Technology, Ocean University of China, 238 Songling Rd, 266100 Shandong, China
| | - Hao Liu
- College of Computer Science and Technology, Ocean University of China, 238 Songling Rd, 266100 Shandong, China
| |
Collapse
|
4
|
An Y, Lim J, Glavatskikh M, Wang X, Norris-Drouin J, Hardy PB, Leisner TM, Pearce KH, Kireev D. In silico fragment-based discovery of CIB1-directed anti-tumor agents by FRASE-bot. Nat Commun 2024; 15:5564. [PMID: 38956119 PMCID: PMC11219766 DOI: 10.1038/s41467-024-49892-9] [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: 07/23/2023] [Accepted: 06/19/2024] [Indexed: 07/04/2024] Open
Abstract
Chemical probes are an indispensable tool for translating biological discoveries into new therapies, though are increasingly difficult to identify since novel therapeutic targets are often hard-to-drug proteins. We introduce FRASE-based hit-finding robot (FRASE-bot), to expedite drug discovery for unconventional therapeutic targets. FRASE-bot mines available 3D structures of ligand-protein complexes to create a database of FRAgments in Structural Environments (FRASE). The FRASE database can be screened to identify structural environments similar to those in the target protein and seed the target structure with relevant ligand fragments. A neural network model is used to retain fragments with the highest likelihood of being native binders. The seeded fragments then inform ultra-large-scale virtual screening of commercially available compounds. We apply FRASE-bot to identify ligands for Calcium and Integrin Binding protein 1 (CIB1), a promising drug target implicated in triple negative breast cancer. FRASE-based virtual screening identifies a small-molecule CIB1 ligand (with binding confirmed in a TR-FRET assay) showing specific cell-killing activity in CIB1-dependent cancer cells, but not in CIB1-depletion-insensitive cells.
Collapse
Affiliation(s)
- Yi An
- Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27513, USA
| | - Jiwoong Lim
- Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27513, USA
| | - Marta Glavatskikh
- Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27513, USA
| | - Xiaowen Wang
- Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27513, USA
- Chemistry department, University of Missouri, Columbia, Columbia, MO, 65211, USA
| | - Jacqueline Norris-Drouin
- Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27513, USA
| | - P Brian Hardy
- Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27513, USA
| | - Tina M Leisner
- Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27513, USA
| | - Kenneth H Pearce
- Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27513, USA.
| | - Dmitri Kireev
- Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27513, USA.
- Chemistry department, University of Missouri, Columbia, Columbia, MO, 65211, USA.
| |
Collapse
|
5
|
Elasbali AM, Al-Soud WA, Elfaki EM, Alanazi HH, Alharbi B, Alharethi SH, Anwer K, Mohammad T, Hassan MI. Identification of novel c-Kit inhibitors from natural sources using virtual screening and molecular dynamics simulations. J Biomol Struct Dyn 2024; 42:5982-5994. [PMID: 37403288 DOI: 10.1080/07391102.2023.2231547] [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: 04/09/2023] [Accepted: 06/24/2023] [Indexed: 07/06/2023]
Abstract
The Mast/Stem cell growth factor receptor Kit (c-Kit), a Proto-oncogene c-Kit, is a tyrosine-protein kinase involved in cell differentiation, proliferation, migration, and survival. Its role in developing certain cancers, particularly gastrointestinal stromal tumors (GISTs) and acute myeloid leukemia (AML), makes it an attractive therapeutic target. Several small molecule inhibitors targeting c-Kit have been developed and approved for clinical use. Recent studies have focused on identifying and optimizing natural compounds as c-Kit inhibitors employing virtual screening. Still, drug resistance, off-target side effects, and variability in patient response remain significant challenges. From this perspective, phytochemicals could be an important resource for discovering novel c-Kit inhibitors with less toxicity, improved efficacy, and high specificity. This study aimed to uncover possible c-Kit inhibitors by utilizing a structure-based virtual screening of active phytoconstituents from Indian medicinal plants. Through the screening stages, two promising candidates, Anilinonaphthalene and Licoflavonol, were chosen based on their drug-like features and ability to bind to c-Kit. These chosen candidates were subjected to all-atom molecular dynamics (MD) simulations to evaluate their stability and interaction with c-Kit. The selected compounds Anilinonaphthalene from Daucus carota and Licoflavonol from Glycyrrhiza glabra showed their potential to act as selective binding partners of c-Kit. Our results suggest that the identified phytoconstituents could serve as a starting point to develop novel c-Kit inhibitors for developing new and effective therapies against multiple cancers, including GISTs and AML. The use of virtual screening and MD simulations provides a rational approach to discovering potential drug candidates from natural sources.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Abdelbaset Mohamed Elasbali
- Department of Clinical Laboratory Science, College of Applied Sciences-Qurayyat, Jouf University, Sakakah, Saudi Arabia
- Health Sciences Research Unit, Jouf University, Sakakah, Saudi Arabia
| | - Waleed Abu Al-Soud
- Department of Clinical Laboratory Science, College of Applied Sciences-Sakaka, Jouf University, Sakakah, Saudi Arabia
| | - Elyasa Mustafa Elfaki
- Department of Clinical Laboratory Science, College of Applied Sciences-Qurayyat, Jouf University, Sakakah, Saudi Arabia
| | - Hamad H Alanazi
- Department of Clinical Laboratory Science, College of Applied Sciences-Qurayyat, Jouf University, Sakakah, Saudi Arabia
| | - Bandar Alharbi
- Department of Clinical Laboratory, College of Applied Medical Sciences, University of Hail, Hail, Saudi Arabia
| | - Salem Hussain Alharethi
- Department of Biological Science, College of Arts and Science, Najran University, Najran, Saudi Arabia
| | - Khalid Anwer
- Department of Botany, C. M. Science College, L. N. Mithila University, Darbhanga, India
| | - Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| |
Collapse
|
6
|
Peralta-Moreno MN, Mena Y, Ortega-Alarcon D, Jimenez-Alesanco A, Vega S, Abian O, Velazquez-Campoy A, Thomson TM, Pinto M, Granadino-Roldán JM, Santos Tomas M, Perez JJ, Rubio-Martinez J. Shedding Light on Dark Chemical Matter: The Discovery of a SARS-CoV-2 M pro Main Protease Inhibitor through Intensive Virtual Screening and In Vitro Evaluation. Int J Mol Sci 2024; 25:6119. [PMID: 38892306 PMCID: PMC11172690 DOI: 10.3390/ijms25116119] [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: 05/01/2024] [Revised: 05/23/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
The development of specific antiviral therapies targeting SARS-CoV-2 remains fundamental because of the continued high incidence of COVID-19 and limited accessibility to antivirals in some countries. In this context, dark chemical matter (DCM), a set of drug-like compounds with outstanding selectivity profiles that have never shown bioactivity despite being extensively assayed, appears to be an excellent starting point for drug development. Accordingly, in this study, we performed a high-throughput screening to identify inhibitors of the SARS-CoV-2 main protease (Mpro) using DCM compounds as ligands. Multiple receptors and two different docking scoring functions were employed to identify the best molecular docking poses. The selected structures were subjected to extensive conventional and Gaussian accelerated molecular dynamics. From the results, four compounds with the best molecular behavior and binding energy were selected for experimental testing, one of which presented inhibitory activity with a Ki value of 48 ± 5 μM. Through virtual screening, we identified a significant starting point for drug development, shedding new light on DCM compounds.
Collapse
Affiliation(s)
- Maria Nuria Peralta-Moreno
- Department of Materials Science and Physical Chemistry, Institut de Recerca en Quimica Teòrica i Computacional (IQTCUB), University of Barcelona (UB), 08028 Barcelona, Spain; (M.N.P.-M.); (Y.M.)
| | - Yago Mena
- Department of Materials Science and Physical Chemistry, Institut de Recerca en Quimica Teòrica i Computacional (IQTCUB), University of Barcelona (UB), 08028 Barcelona, Spain; (M.N.P.-M.); (Y.M.)
| | - David Ortega-Alarcon
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain; (D.O.-A.); (A.J.-A.); (S.V.); (O.A.); (A.V.-C.)
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Ana Jimenez-Alesanco
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain; (D.O.-A.); (A.J.-A.); (S.V.); (O.A.); (A.V.-C.)
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Sonia Vega
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain; (D.O.-A.); (A.J.-A.); (S.V.); (O.A.); (A.V.-C.)
| | - Olga Abian
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain; (D.O.-A.); (A.J.-A.); (S.V.); (O.A.); (A.V.-C.)
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
- Instituto de Investigación Sanitaria de Aragón (IIS Aragon), 50009 Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas Digestivas (CIBERehd), 28029 Madrid, Spain;
| | - Adrian Velazquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain; (D.O.-A.); (A.J.-A.); (S.V.); (O.A.); (A.V.-C.)
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
- Instituto de Investigación Sanitaria de Aragón (IIS Aragon), 50009 Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas Digestivas (CIBERehd), 28029 Madrid, Spain;
| | - Timothy M. Thomson
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas Digestivas (CIBERehd), 28029 Madrid, Spain;
- Institute of Molecular Biology of Barcelona (IBMB-CSIC), 08028 Barcelona, Spain
- Instituto de investigaciones de la Altura, Universidad Peruana Cayetano Heredia, Av. Honorio Delgado 430, Lima 15102, Peru
| | - Marta Pinto
- AbbVie Deutschland GmbH & Co. KG, Computational Drug Discovery, Knollstrasse, 67061 Ludwigshafen, Germany;
| | - José M. Granadino-Roldán
- Departamento de Química Física y Analítica, Facultad de Ciencias Experimentales, Universidad de Jaén, Campus “Las Lagunillas” s/n, 23071 Jaén, Spain;
| | - Maria Santos Tomas
- Department of Architecture Technology, Universitat Politecnica de Catalunya (UPC), Av. Diagonal 649, 08028 Barcelona, Spain;
| | - Juan J. Perez
- Department of Chemical Engineering, Universitat Politecnica de Catalunya (UPC), Barcelona Tech. Av. Diagonal, 647, 08028 Barcelona, Spain;
| | - Jaime Rubio-Martinez
- Department of Materials Science and Physical Chemistry, Institut de Recerca en Quimica Teòrica i Computacional (IQTCUB), University of Barcelona (UB), 08028 Barcelona, Spain; (M.N.P.-M.); (Y.M.)
| |
Collapse
|
7
|
Bayarsaikhan B, Zsidó BZ, Börzsei R, Hetényi C. Efficient Refinement of Complex Structures of Flexible Histone Peptides Using Post-Docking Molecular Dynamics Protocols. Int J Mol Sci 2024; 25:5945. [PMID: 38892133 PMCID: PMC11172440 DOI: 10.3390/ijms25115945] [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: 04/24/2024] [Revised: 05/26/2024] [Accepted: 05/27/2024] [Indexed: 06/21/2024] Open
Abstract
Histones are keys to many epigenetic events and their complexes have therapeutic and diagnostic importance. The determination of the structures of histone complexes is fundamental in the design of new drugs. Computational molecular docking is widely used for the prediction of target-ligand complexes. Large, linear peptides like the tail regions of histones are challenging ligands for docking due to their large conformational flexibility, extensive hydration, and weak interactions with the shallow binding pockets of their reader proteins. Thus, fast docking methods often fail to produce complex structures of such peptide ligands at a level appropriate for drug design. To address this challenge, and improve the structural quality of the docked complexes, post-docking refinement has been applied using various molecular dynamics (MD) approaches. However, a final consensus has not been reached on the desired MD refinement protocol. In this present study, MD refinement strategies were systematically explored on a set of problematic complexes of histone peptide ligands with relatively large errors in their docked geometries. Six protocols were compared that differ in their MD simulation parameters. In all cases, pre-MD hydration of the complex interface regions was applied to avoid the unwanted presence of empty cavities. The best-performing protocol achieved a median of 32% improvement over the docked structures in terms of the change in root mean squared deviations from the experimental references. The influence of structural factors and explicit hydration on the performance of post-docking MD refinements are also discussed to help with their implementation in future methods and applications.
Collapse
Affiliation(s)
- Bayartsetseg Bayarsaikhan
- Pharmacoinformatics Unit, Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, H-7624 Pécs, Hungary; (B.B.); (B.Z.Z.); (R.B.)
| | - Balázs Zoltán Zsidó
- Pharmacoinformatics Unit, Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, H-7624 Pécs, Hungary; (B.B.); (B.Z.Z.); (R.B.)
| | - Rita Börzsei
- Pharmacoinformatics Unit, Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, H-7624 Pécs, Hungary; (B.B.); (B.Z.Z.); (R.B.)
| | - Csaba Hetényi
- Pharmacoinformatics Unit, Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, H-7624 Pécs, Hungary; (B.B.); (B.Z.Z.); (R.B.)
- National Laboratory for Drug Research and Development, Magyar tudósok krt. 2, H-1117 Budapest, Hungary
| |
Collapse
|
8
|
Lu Y, Feng S, Zhao Y, Wang Y, Diao M, Liang Y, Zhang T. Comparison of interactions between alpha-lactalbumin and three protopanaxadiol ginsenosides: Impacts on the structure and antitumor properties. Food Chem 2024; 439:138046. [PMID: 38029562 DOI: 10.1016/j.foodchem.2023.138046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 11/16/2023] [Accepted: 11/18/2023] [Indexed: 12/01/2023]
Abstract
In this research, interactions between α-lactalbumin (ALA) and three protopanaxadiol ginsenosides [20(S)-Rg3, 20(S)-Rh2, and 20(S)-PPD] were compared to explore the effects of similar ligand on structure and cytotoxicity of ALA. Multi-spectroscopy revealed the binding between ALA and ginsenoside changed the conformation of ALA, which related to different structures and solubility of ligands. Scanning electron microscope illustrated that all ALA-ginsenoside complexes exhibited denser structures via hydrophobic interactions. Additionally, the cytotoxic experiments confirmed that the cytotoxicity of ginsenoside was enhanced after binding with ALA. Molecular docking showed all three ginsenosides were bound to the sulcus depression region of ALA via hydrogen bonding and hydrophobic interaction. Furthermore, molecular dynamics simulation elucidated the precise binding sites and pertinent system properties. Among all three composite systems, 20(S)-Rh2 had optimal binding affinity. These findings enhanced understanding of the synergistic utilization of ALA and ginsenosides as functional ingredients in food, medicine, and cosmetics.
Collapse
Affiliation(s)
- Yitong Lu
- College of Food Science and Engineering, Jilin University, Changchun 130062, China.
| | - Sitong Feng
- College of Food Science and Engineering, Jilin University, Changchun 130062, China
| | - Yueying Zhao
- College of Food Science and Engineering, Jilin University, Changchun 130062, China.
| | - Yingyi Wang
- College of Food Science and Engineering, Jilin University, Changchun 130062, China
| | - Mengxue Diao
- College of Food Science and Engineering, Jilin University, Changchun 130062, China
| | - Yuan Liang
- College of Food Science and Engineering, Jilin University, Changchun 130062, China.
| | - Tiehua Zhang
- College of Food Science and Engineering, Jilin University, Changchun 130062, China.
| |
Collapse
|
9
|
Jana A, Naga R, Saha S, Griñán-Ferré C, Banerjee DR. Integration of ligand and structure-based pharmacophore screening for the identification of novel natural leads against Euchromatic histone lysine methyltransferase 2 (EHMT2/G9a). J Biomol Struct Dyn 2024; 42:3535-3562. [PMID: 37216299 DOI: 10.1080/07391102.2023.2213346] [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: 02/14/2023] [Accepted: 05/08/2023] [Indexed: 05/24/2023]
Abstract
Herein, we report a blended ligand and structure-based pharmacophore screening approach to identify new natural leads against the Protein Lysine Methyltransferase 2 (EHMT2/G9a). The EHMT2/G9a has been associated with Cancer, Alzheimer's, and aging and is considered an emerging drug target having no clinically passed inhibitor. Purposefully, we developed the ligand-based pharmacophore (Pharmacophore-L) based on the common features of known inhibitors and the structure-based pharmacophore (Pharmacophore-S) based on the interaction profile of available crystal structures. The Pharmacophore-L and Pharmacophore-S were subjected to multiple tiers of validations and utilized in combination for the screening of total 741543 compounds coming from multiple databases. Additional layers of stringency were applied in the screening process to test drug-likeness (using Lipinski's rule, Veber's rule, SMARTS and ADMET filtration), to rule out any toxicity (TOPKAT analysis). The interaction profiles, stabilities, and comparative analysis against the reference were carried out by flexible docking, MD simulation, and MM-GBSA analysis, which finally led to three leads as potential inhibitors of G9a.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Abhisek Jana
- Department of Chemistry, National Institute of Technology Durgapur, Durgapur, India
| | - Rahul Naga
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, India
| | - Sougata Saha
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, India
| | - Christian Griñán-Ferré
- Department of Pharmacology and Therapeutic Chemistry, Institut de Neurociències, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación en Red, Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - Deb Ranjan Banerjee
- Department of Chemistry, National Institute of Technology Durgapur, Durgapur, India
| |
Collapse
|
10
|
Avilés-Alía AI, Zulaica J, Perez JJ, Rubio-Martínez J, Geller R, Granadino-Roldán JM. The Discovery of inhibitors of the SARS-CoV-2 S protein through computational drug repurposing. Comput Biol Med 2024; 171:108163. [PMID: 38417382 DOI: 10.1016/j.compbiomed.2024.108163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/08/2024] [Accepted: 02/13/2024] [Indexed: 03/01/2024]
Abstract
SARS-CoV-2 must bind its principal receptor, ACE2, on the target cell to initiate infection. This interaction is largely driven by the receptor binding domain (RBD) of the viral Spike (S) protein. Accordingly, antiviral compounds that can block RBD/ACE2 interactions can constitute promising antiviral agents. To identify such molecules, we performed a virtual screening of the Selleck FDA approved drugs and the Selleck database of Natural Products using a multistep computational procedure. An initial set of candidates was identified from an ensemble docking process using representative structures determined from the analysis of four 3 μ s molecular dynamics trajectories of the RBD/ACE2 complex. Two procedures were used to construct an initial set of candidates including a standard and a pharmacophore guided docking procedure. The initial set was subsequently subjected to a multistep sieving process to reduce the number of candidates to be tested experimentally, using increasingly demanding computational procedures, including the calculation of the binding free energy computed using the MMPBSA and MMGBSA methods. After the sieving process, a final list of 10 candidates was proposed, compounds which were subsequently purchased and tested ex-vivo. The results identified estradiol cypionate and telmisartan as inhibitors of SARS-CoV-2 entry into cells. Our findings demonstrate that the methodology presented here enables the discovery of inhibitors targeting viruses for which high-resolution structures are available.
Collapse
Affiliation(s)
- Ana Isabel Avilés-Alía
- Institute for Integrative Systems Biology (I2SysBio, UV-CSIC), C/ Catedrático José Beltrán, 2, 46980, Paterna, Valencia, Spain
| | - Joao Zulaica
- Institute for Integrative Systems Biology (I2SysBio, UV-CSIC), C/ Catedrático José Beltrán, 2, 46980, Paterna, Valencia, Spain
| | - Juan J Perez
- Department of Chemical Engineering, Universitat Politecnica de Catalunya- Barcelona Tech, 08028, Barcelona, Spain
| | - Jaime Rubio-Martínez
- Department of Materials Science and Physical Chemistry, University of Barcelona and the Institut de Recerca en Quimica Teorica i Computacional (IQTCUB), 08028, Barcelona, Spain
| | - Ron Geller
- Institute for Integrative Systems Biology (I2SysBio, UV-CSIC), C/ Catedrático José Beltrán, 2, 46980, Paterna, Valencia, Spain.
| | - José M Granadino-Roldán
- Departamento de Química Física y Analítica. Universidad de Jaén, Campus "Las Lagunillas" s/n, 23071, Jaén, Spain.
| |
Collapse
|
11
|
Zhang Y, Miao D, Liu S, Hao X. Revealing the binding mechanism of BACE1 inhibitors through molecular dynamics simulations. J Biomol Struct Dyn 2024:1-13. [PMID: 38375603 DOI: 10.1080/07391102.2024.2319676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 02/11/2024] [Indexed: 02/21/2024]
Abstract
Alzheimer's disease is a debilitating neurodegenerative disorder, and the Beta-Site Amyloid Precursor Protein Cleaving Enzyme 1 (BACE1) is a key therapeutic target in its treatment. This study employs molecular dynamics simulations and binding energy analysis to investigate the binding interactions between BACE1 and four selected small molecules: CNP520, D9W, NB641, and NB360. The binding model analysis indicates that the binding of BACE1 with four molecules are stable, except the loop regions show significant fluctuation. The binding free energy analyses reveal that NB360 exhibits the highest binding affinity with BACE1, surpassing other molecules (CNP520, D9W, and NB641). Detailed energy component assessments highlight the critical roles of electrostatic interactions and van der Waals forces in the binding process. Furthermore, residue contribution analysis identifies key amino acids influencing the binding process across all systems. Hydrogen bond analysis reveals a limited number of bonds between BACE1 and each small molecule, highlighting the importance of structural modifications to enable more stable hydrogen bonds. This research provides valuable insights into the molecular mechanisms of potential Alzheimer's disease therapeutics, guiding the way for improved drug design and the development of effective treatments targeting BACE1.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Yanjun Zhang
- School of Mathematics & Physics, Hebei University of Engineering, Handan, China
| | - Dongqiang Miao
- School of Mathematics & Physics, Hebei University of Engineering, Handan, China
| | - Senchen Liu
- School of Mathematics & Physics, Hebei University of Engineering, Handan, China
| | - Xiafei Hao
- Medical College, Hebei University of Engineering, Handan, China
| |
Collapse
|
12
|
Isert C, Atz K, Riniker S, Schneider G. Exploring protein-ligand binding affinity prediction with electron density-based geometric deep learning. RSC Adv 2024; 14:4492-4502. [PMID: 38312732 PMCID: PMC10835705 DOI: 10.1039/d3ra08650j] [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: 12/18/2023] [Accepted: 01/19/2024] [Indexed: 02/06/2024] Open
Abstract
Rational structure-based drug design relies on accurate predictions of protein-ligand binding affinity from structural molecular information. Although deep learning-based methods for predicting binding affinity have shown promise in computational drug design, certain approaches have faced criticism for their potential to inadequately capture the fundamental physical interactions between ligands and their macromolecular targets or for being susceptible to dataset biases. Herein, we propose to include bond-critical points based on the electron density of a protein-ligand complex as a fundamental physical representation of protein-ligand interactions. Employing a geometric deep learning model, we explore the usefulness of these bond-critical points to predict absolute binding affinities of protein-ligand complexes, benchmark model performance against existing methods, and provide a critical analysis of this new approach. The models achieved root-mean-squared errors of 1.4-1.8 log units on the PDBbind dataset, and 1.0-1.7 log units on the PDE10A dataset, not indicating significant advantages over benchmark methods, and thus rendering the utility of electron density for deep learning models context-dependent. The relationship between intermolecular electron density and corresponding binding affinity was analyzed, and Pearson correlation coefficients r > 0.7 were obtained for several macromolecular targets.
Collapse
Affiliation(s)
- Clemens Isert
- ETH Zurich, Department of Chemistry and Applied Biosciences Vladimir-Prelog-Weg 4 8093 Zurich Switzerland +41 44 633 73 27
| | - Kenneth Atz
- ETH Zurich, Department of Chemistry and Applied Biosciences Vladimir-Prelog-Weg 4 8093 Zurich Switzerland +41 44 633 73 27
| | - Sereina Riniker
- ETH Zurich, Department of Chemistry and Applied Biosciences Vladimir-Prelog-Weg 4 8093 Zurich Switzerland +41 44 633 73 27
| | - Gisbert Schneider
- ETH Zurich, Department of Chemistry and Applied Biosciences Vladimir-Prelog-Weg 4 8093 Zurich Switzerland +41 44 633 73 27
| |
Collapse
|
13
|
Sahoo S, Lee HK, Shin D. Structure-based virtual screening and molecular dynamics studies to explore potential natural inhibitors against 3C protease of foot-and-mouth disease virus. Front Vet Sci 2024; 10:1340126. [PMID: 38298458 PMCID: PMC10827980 DOI: 10.3389/fvets.2023.1340126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 12/27/2023] [Indexed: 02/02/2024] Open
Abstract
Foot-and-mouth disease (FMD) is a highly infectious animal disease caused by foot-and-mouth disease virus (FMDV) and primarily infects cloven-hoofed animals such as cattle, sheep, goats, and pigs. It has become a significant health concern in global livestock industries because of diverse serotypes, high mutation rates, and contagious nature. There is no specific antiviral treatment available for FMD. Hence, based on the importance of 3C protease in FMDV viral replication and pathogenesis, we have employed a structure-based virtual screening method by targeting 3C protease with a natural compounds dataset (n = 69,040) from the InterBioScreen database. Virtual screening results identified five potential compounds, STOCK1N-62634, STOCK1N-96109, STOCK1N-94672, STOCK1N-89819, and STOCK1N-80570, with a binding affinity of -9.576 kcal/mol, -8.1 kcal/mol, -7.744 kcal/mol, -7.647 kcal/mol, and - 7.778 kcal/mol, respectively. The compounds were further validated through physiochemical properties and density functional theory (DFT). Subsequently, the comparative 300-ns MD simulation of all five complexes exhibited overall structural stability from various MD analyses such as root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), solvent accessible surface area (SASA), H-bonds, principal component analysis (PCA), and free energy landscape (FEL). Furthermore, MM-PBSA calculation suggests that all five compounds, particularly STOCK1N-62634, STOCK1N-96109, and STOCK1N-94672, can be considered as potential inhibitors because of their strong binding affinity toward 3C protease. Thus, we hope that these identified compounds can be studied extensively to develop natural therapeutics for the better management of FMD.
Collapse
Affiliation(s)
- Sthitaprajna Sahoo
- Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju, Republic of Korea
| | - Hak-Kyo Lee
- Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju, Republic of Korea
- Department of Animal Biotechnology, Jeonbuk National University, Jeonju, Republic of Korea
| | - Donghyun Shin
- Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju, Republic of Korea
| |
Collapse
|
14
|
Valdivia A, Luque FJ, Llabrés S. Binding of Cholesterol to the N-Terminal Domain of the NPC1L1 Transporter: Analysis of the Epimerization-Related Binding Selectivity and Loop Mutations. J Chem Inf Model 2024; 64:189-204. [PMID: 38152929 PMCID: PMC10777396 DOI: 10.1021/acs.jcim.3c01319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 12/29/2023]
Abstract
Cholesterol is a fat-like substance with a pivotal physiological relevance in humans, and its homeostasis is tightly regulated by various cellular processes, including the import in the small intestine and the reabsorption in the biliary ducts by the Niemann-Pick C1 Like 1 (NPC1L1) importer. NPC1L1 can mediate the absorption of a variety of sterols but strikingly exhibits a large sensitivity to cholesterol epimerization. This study examines the molecular basis of the epimerization-related selective binding of cholesterol by combining extended unbiased molecular dynamics simulations of the apo and holo species of the N-terminal domain of wild-type NPC1L1, in conjunction with relative binding free energy, umbrella sampling, and well-tempered metadynamics calculations. The analysis of the results discloses the existence of two distinct binding modes for cholesterol and epi-cholesterol. The former binds deeper in the cavity, forming key hydrogen-bond interactions with Q95, S56, and a water molecule. In contrast, epi-cholesterol is shifted ca. 3 Å to the mouth of the cavity and the transition to the Q95 site is prevented by an energetic barrier of 4.1 kcal·mol-1. Thus, the configuration of the hydroxyl group of cholesterol, together with the presence of a structural water molecule, is a key feature for effective absorption. Finally, whereas these findings may seemingly be challenged by single-point mutations that impair cholesterol transport but have a mild impact on the binding of cholesterol to the Q95 binding site, our results reveal that they have a drastic influence on the conformational landscape of the α8/β7 loop in the apo species compared to the wild-type protein. Overall, the results give support to the functional role played by the α8/β7 loop in regulating the access of ligands to NPC1L1, and hence to interpreting the impact of these mutations on diseases related to disruption of sterol absorption, paving the way to understanding certain physiological dysfunctions.
Collapse
Affiliation(s)
- Aitor Valdivia
- Departament
de Nutrició, Ciències de l′Alimentació
i Gastronomia, Facultat de Farmàcia
i Ciències de l′Alimentació—Campus Torribera,
Universitat de Barcelona, Prat de la Riba 171, 08921 Santa Coloma de Gramenet, Spain
- Institut
de Biomedicina (IBUB), Universitat de Barcelona, 08028 Barcelona, Spain
| | - F. Javier Luque
- Departament
de Nutrició, Ciències de l′Alimentació
i Gastronomia, Facultat de Farmàcia
i Ciències de l′Alimentació—Campus Torribera,
Universitat de Barcelona, Prat de la Riba 171, 08921 Santa Coloma de Gramenet, Spain
- Institut
de Biomedicina (IBUB), Universitat de Barcelona, 08028 Barcelona, Spain
- Institut
de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08921 Barcelona, Spain
| | - Salomé Llabrés
- Departament
de Nutrició, Ciències de l′Alimentació
i Gastronomia, Facultat de Farmàcia
i Ciències de l′Alimentació—Campus Torribera,
Universitat de Barcelona, Prat de la Riba 171, 08921 Santa Coloma de Gramenet, Spain
- Institut
de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08921 Barcelona, Spain
| |
Collapse
|
15
|
Galati S, Di Stefano M, Bertini S, Granchi C, Giordano A, Gado F, Macchia M, Tuccinardi T, Poli G. Identification of New GSK3β Inhibitors through a Consensus Machine Learning-Based Virtual Screening. Int J Mol Sci 2023; 24:17233. [PMID: 38139062 PMCID: PMC10743990 DOI: 10.3390/ijms242417233] [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: 11/13/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
Glycogen synthase kinase-3 beta (GSK3β) is a serine/threonine kinase that plays key roles in glycogen metabolism, Wnt/β-catenin signaling cascade, synaptic modulation, and multiple autophagy-related signaling pathways. GSK3β is an attractive target for drug discovery since its aberrant activity is involved in the development of neurodegenerative diseases such as Alzheimer's and Parkinson's disease. In the present study, multiple machine learning models aimed at identifying novel GSK3β inhibitors were developed and evaluated for their predictive reliability. The most powerful models were combined in a consensus approach, which was used to screen about 2 million commercial compounds. Our consensus machine learning-based virtual screening led to the identification of compounds G1 and G4, which showed inhibitory activity against GSK3β in the low-micromolar and sub-micromolar range, respectively. These results demonstrated the reliability of our virtual screening approach. Moreover, docking and molecular dynamics simulation studies were employed for predicting reliable binding modes for G1 and G4, which represent two valuable starting points for future hit-to-lead and lead optimization studies.
Collapse
Affiliation(s)
- Salvatore Galati
- Department of Pharmacy, University of Pisa, 56126 Pisa, Italy; (S.G.); (M.D.S.); (S.B.); (C.G.); (M.M.); (G.P.)
| | - Miriana Di Stefano
- Department of Pharmacy, University of Pisa, 56126 Pisa, Italy; (S.G.); (M.D.S.); (S.B.); (C.G.); (M.M.); (G.P.)
- Department of Life Sciences, University of Siena, 53100 Siena, Italy
| | - Simone Bertini
- Department of Pharmacy, University of Pisa, 56126 Pisa, Italy; (S.G.); (M.D.S.); (S.B.); (C.G.); (M.M.); (G.P.)
| | - Carlotta Granchi
- Department of Pharmacy, University of Pisa, 56126 Pisa, Italy; (S.G.); (M.D.S.); (S.B.); (C.G.); (M.M.); (G.P.)
| | - Antonio Giordano
- Sbarro Institute for Cancer Research and Molecular Medicine Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA;
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
| | - Francesca Gado
- Department of Pharmaceutical Sciences, University of Milan, 20133 Milan, Italy;
| | - Marco Macchia
- Department of Pharmacy, University of Pisa, 56126 Pisa, Italy; (S.G.); (M.D.S.); (S.B.); (C.G.); (M.M.); (G.P.)
| | - Tiziano Tuccinardi
- Department of Pharmacy, University of Pisa, 56126 Pisa, Italy; (S.G.); (M.D.S.); (S.B.); (C.G.); (M.M.); (G.P.)
| | - Giulio Poli
- Department of Pharmacy, University of Pisa, 56126 Pisa, Italy; (S.G.); (M.D.S.); (S.B.); (C.G.); (M.M.); (G.P.)
| |
Collapse
|
16
|
Ge H, Ji B, Fang J, Wang J, Li J, Wang J. Discovery of Potent and Selective CB2 Agonists Utilizing a Function-Based Computational Screening Protocol. ACS Chem Neurosci 2023; 14:3941-3958. [PMID: 37823773 PMCID: PMC10623575 DOI: 10.1021/acschemneuro.3c00580] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 09/22/2023] [Indexed: 10/13/2023] Open
Abstract
Nowadays, the identification of agonists and antagonists represents a great challenge in computer-aided drug design. In this work, we developed a computational protocol enabling us to design/screen novel chemicals that are likely to serve as selective CB2 agonists. The principle of this protocol is that by calculating the ligand-residue interaction profile (LRIP) of a ligand binding to a specific target, the agonist-antagonist function of a compound is then able to be determined after statistical analysis and free energy calculations. This computational protocol was successfully applied in CB2 agonist development starting from a lead compound, and a success rate of 70% was achieved. The functions of the synthesized derivatives were determined by in vitro functional assays. Moreover, the identified potent CB2 agonists and antagonists strongly interact with the key residues identified using the already known potent CB2 agonists/antagonists. The analysis of the interaction profile of compound 6, a potent agonist, showed strong interactions with F2.61, I186, and F2.64, while compound 39, a potent antagonist, showed strong interactions with L17, W6.48, V6.51, and C7.42. Still, some residues including V3.32, T3.33, S7.39, F183, W5.43, and I3.29 are hotspots for both CB2 agonists and antagonists. More significantly, we identified three hotspot residues in the loop, including I186 for agonists, L17 for antagonists, and F183 for both. These hotspot residues are typically not considered in CB1/CB2 rational ligand design. In conclusion, LRIP is a useful concept in rationally designing a compound to possess a certain function.
Collapse
Affiliation(s)
- Haixia Ge
- School
of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Beihong Ji
- Department
of Pharmaceutical Sciences and Computational Chemical Genomics Screening
Center, School of Pharmacy, University of
Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Jiahui Fang
- Chinese
Academy of Sciences Key Laboratory of Receptor Research, National
Center for Drug Screening, Shanghai Institute
of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jiayang Wang
- School
of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Jing Li
- Chinese
Academy of Sciences Key Laboratory of Receptor Research, National
Center for Drug Screening, Shanghai Institute
of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Junmei Wang
- Department
of Pharmaceutical Sciences and Computational Chemical Genomics Screening
Center, School of Pharmacy, University of
Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| |
Collapse
|
17
|
Gautam P, Bisht P, Gautam A, Gupta GD, Singh R, Verma SK. A comprehension on structure guided alignment dependent 3D-QSAR modelling, and molecular dynamics simulation on 2,4-thiazolidinediones as aldose reductase inhibitors for the management of diabetic complications. J Biomol Struct Dyn 2023:1-20. [PMID: 37904329 DOI: 10.1080/07391102.2023.2275190] [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: 06/27/2023] [Accepted: 10/20/2023] [Indexed: 11/01/2023]
Abstract
Aldose reductase is an oxo-reductase enzyme belonging to the aldo-keto reductase class. Compounds having thiazolidine-2,4-dione scaffold are reported as potential aldose reductase inhibitors for diabetic complications. The present work uses structure-guided alignment-dependent Gaussian field- and atom-based 3D-QSAR on a dataset of 84 molecules. 3D-QSAR studies on two sets of dataset alignment have been carried out to understand the favourable and unfavourable structural features influencing the affinity of these inhibitors towards the enzyme. Using common pharmacophore hypotheses, the five-point pharmacophores for aldose reductase favourable features were generated. The molecular dynamics simulations (up to 100 ns) were performed for the potent molecule from each alignment set (compounds 24 and 65) compared to reference standard tolrestat and epalrestat to study target-ligand complexes' binding energy and stability. Compound 65 was most stable with better interactions in the aldose reductase binding pocket than tolrestat. The MM-PBSA study suggests compound 65 possessed better binding energy than reference standard tolrestat, i.e. -87.437 ± 19.728 and -73.424 ± 12.502 kJ/mol, respectively. The generated 3D-QSAR models provide information about structure-activity relationships and ligand-target binding energy. Target-specific stability data from MD simulation would be helpful for rational compound design with better aldose reductase activity.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Priyadarshi Gautam
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga, India
| | - Priya Bisht
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga, India
| | - Anupam Gautam
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany
- International Max Planck Research School "From Molecules to Organisms", Max Planck Institute for Biology Tübingen, Tübingen, Germany
- Cluster of Excellence: EXC 2124: Controlling Microbes to Fight Infection, University of Tübingen, Tübingen, Germany
| | | | - Rajveer Singh
- Department of Pharmacognosy, ISF College of Pharmacy, Moga, India
| | - Sant Kumar Verma
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga, India
| |
Collapse
|
18
|
Ali Alshehri S, Alsayari A, Wahab S, H Alqarni M, Sweilam SH, Khalid M. Prediction of molecular interaction of Phosphodiesterase 10A inhibition by natural compounds: insights from structure-based screening and molecular dynamics simulations. J Biomol Struct Dyn 2023:1-12. [PMID: 37850684 DOI: 10.1080/07391102.2023.2270756] [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: 03/29/2023] [Accepted: 10/08/2023] [Indexed: 10/19/2023]
Abstract
Phosphodiesterase 10 A (PDE10A) is an enzyme that regulates cyclic adenosine monophosphate (cAMP) and cyclic guanosine monophosphate (cGMP) levels in the brain, particularly in the striatum, which plays a critical role in movement control and reward processing. Inhibition of PDE10A can increase cAMP and cGMP levels, improving neuronal signaling and reducing symptoms of neuropsychiatric disorders such as schizophrenia, Huntington's disease, and Parkinson's disease. In this study, a structure-based virtual screening was conducted to identify potential anti-neuropsychiatric disorders compounds from phytoconstituents in the IMPPAT database. The ligands were docked against PDE10A, resulting in 40 compounds with appreciable docking scores. These 40 compounds underwent further ADMET predictions and drug likeliness, resulting in five potential compounds. Finally, based on the specific interactions, two compounds (Colladonin and Isopongachromene), were subjected to molecular dynamics (MD) simulation and MM-PBSA studies. The MM-PBSA analysis validated and captured the intermolecular interactions, indicating that Colladonin and Isopongachromene had appreciable binding affinities of -155.60 kJ.mol-1 and -108.28 kJ.mol-1, respectively and were promising candidates against neuropsychiatric disorders, targeting PDE10A. Overall, this study provides insight into the potential of PDE10A inhibitors as therapeutic agents for treating neuropsychiatric disorders, and Colladonin and Isopongachromene are promising compounds for further development.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Saad Ali Alshehri
- Department of Pharmacognosy, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Abdulrhman Alsayari
- Department of Pharmacognosy, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Shadma Wahab
- Department of Pharmacognosy, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Mohammed H Alqarni
- Department of Pharmacognosy, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Sherouk Hussein Sweilam
- Department of Pharmacognosy, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Mohammad Khalid
- Department of Pharmacognosy, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| |
Collapse
|
19
|
Majrashi TA, Wahab S, Almoyad MAA, Alkhathami AG, Alshahrani MY. Exploring natural compound, Panicutine as leucine-rich repeat kinase 2 inhibitor against Parkinson's disease: a structure-guided approach. J Biomol Struct Dyn 2023:1-10. [PMID: 37837424 DOI: 10.1080/07391102.2023.2268183] [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: 06/21/2023] [Accepted: 09/29/2023] [Indexed: 10/16/2023]
Abstract
Leucine-rich repeat kinase 2 (LRRK2) is a promising drug target for the therapeutic management of Parkinson's disease (PD) and other neurodegenerative disorders. LRRK2 inhibitors have the potential to modulate neuroinflammation, reduce alpha-synuclein aggregation and improve motor symptoms in PD patients. Although LRRK2 inhibitors are still in the early stages of clinical development, the identification of potent and selective inhibitors through structure-guided approaches provides a promising avenue for the development of effective therapies for PD and other neurodegenerative disorders. In this study, natural compounds from the IMPPAT database were screened using a state-of-the-art computational virtual screening approach to identify potential inhibitors of LRRK2. We carried out a docking screening on a library of natural compounds and identified a few compounds with strong binding affinity, docking score and specificity towards LRRK2 as the top hits. These hits were then subjected to further analysis based on multiple parameters for the Pan-assay interference compounds and their physicochemical and pharmacokinetics evaluation followed by a detailed interaction analysis. After careful evaluation, one natural compound, Panicutine, was identified as a promising candidate for LRRK2 due to its significant affinity and specificity towards the LRRK2 binding pocket. Additionally, it exhibited drug-like properties with blood-brain barrier permeability as determined by ADMET properties. To gain a deeper understanding of the stability and conformational changes of the LRRK2-ligand complex, MD simulations were conducted for 100 nanoseconds under explicit solvent conditions followed by principal component analysis and free energy dynamics. The simulation results demonstrated that the LRRK2-Panicutine complex remained stable throughout the simulation trajectories. Based on these findings, it is concluded that Panicutine has the potential to act as a LRRK2 inhibitor against PD and other neurodegenerative disorders.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Taghreed A Majrashi
- Department of Pharmacognosy, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Shadma Wahab
- Department of Pharmacognosy, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Mohammad Ali Abdullah Almoyad
- Department of Basic Medical Sciences, College of Applied Medical Sciences in Khamis Mushyt, King Khalid University, Abha, Saudi Arabia
| | - Ali Gaithan 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
| |
Collapse
|
20
|
Souza BGD, Choudhary S, Vilela GG, Passos GFS, Costa CACB, Freitas JDD, Coelho GL, Brandão JDA, Anderson L, Bassi ÊJ, Araújo-Júnior JXD, Tomar S, Silva-Júnior EFD. Design, synthesis, antiviral evaluation, and In silico studies of acrylamides targeting nsP2 from Chikungunya virus. Eur J Med Chem 2023; 258:115572. [PMID: 37364511 DOI: 10.1016/j.ejmech.2023.115572] [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: 01/01/2023] [Revised: 06/11/2023] [Accepted: 06/11/2023] [Indexed: 06/28/2023]
Abstract
The Togaviridae family comprises several New- and Old-World Alphaviruses that have been responsible for thousands of human illnesses, including the RNA arbovirus Chikungunya virus (CHIKV). Firstly, it was reported in Tanzania in 1952 but rapidly it spread to several countries from Europe, Asia, and the Americas. Since then, CHIKV has been circulating in diverse countries around the world, leading to increased morbidity rates. Currently, there are no FDA-approved drugs or licensed vaccines to specifically treat CHIKV infections. Thus, there is a lack of alternatives to fight against this viral disease, making it an unmet need. Structurally, CHIKV is composed of five structural proteins (E3, E2, E1, C, and 6k) and four non-structural proteins (nsP1-4), in which nsP2 represents an attractive antiviral target for designing novel inhibitors since it has an essential role in the virus replication and transcription. Herein, we used a rational drug design strategy to select some acrylamide derivatives to be synthesized and evaluated against CHIKV nsP2 and also screened on CHIKV-infected cells. Thus, two regions of modifications were considered for these types of inhibitors, based on a previous study of our group, generating 1560 possible inhibitors. Then, the 24 most promising ones were synthesized and screened by using a FRET-based enzymatic assay protocol targeting CHIKV nsP2, identifying LQM330, 333, 336, and 338 as the most potent inhibitors, with Ki values of 48.6 ± 2.8, 92.3 ± 1.4, 2.3 ± 1.5, and 181.8 ± 2.5 μM, respectively. Still, their Km and Vmax kinetic parameters were also determined, along with their competitive binding modes of CHIKV nsP2 inhibition. Then, ITC analyses revealed KD values of 127, 159, 198, and 218 μM for LQM330, 333, 336, and 338, respectively. Also, their ΔH, ΔS, and ΔG physicochemical parameters were determined. MD simulations demonstrated that these inhibitors present a stable binding mode with nsP2, interacting with important residues of this protease, according to docking analyzes. Moreover, MM/PBSA calculations displayed that van der Waals interactions are mainly responsible for stabilizing the inhibitor-nsP2 complex, and their binding energies corroborated with their Ki values, having -198.7 ± 15.68, -124.8 ± 17.27, -247.4 ± 23.78, and -100.6 ± 19.21 kcal/mol for LQM330, 333, 336, and 338, respectively. Since Sindbis (SINV) nsP2 is similar to CHIKV nsP2, these best inhibitors were screened against SINV-infected cells, and it was verified that LQM330 presented the best result, with an EC50 value of 0.95 ± 0.09 μM. Even at 50 μM concentration, LQM338 was found to be cytotoxic on Vero cells after 48 h. Then, LQM330, 333, and 336 were evaluated against CHIKV-infected cells in antiviral assays, in which LQM330 was found to be the most promising antiviral candidate in this study, exhibiting an EC50 value of 5.2 ± 0.52 μM and SI of 31.78. The intracellular flow cytometry demonstrated that LQM330 is able to reduce the CHIKV cytopathogenic effect on cells, and also reduce the percentage of CHIKV-positive cells from 66.1% ± 7.05 to 35.8% ± 5.78 at 50 μM concentration. Finally, qPCR studies demonstrated that LQM330 was capable of reducing the number of viral RNA copies/μL, suggesting that CHIKV nsP2 is targeted by this inhibitor as its mechanism of action.
Collapse
Affiliation(s)
- Beatriz Gois de Souza
- Laboratory of Medicinal Chemistry, Institute of Pharmaceutical Sciences, Federal University of Alagoas, Lourival Melo Mota Avenue, AC. Simões Campus, 57072-970, Alagoas, Maceió, Brazil
| | - Shweta Choudhary
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, 247667, Uttarakhand, India
| | - Gabriel Gomes Vilela
- Laboratory of Medicinal Chemistry, Institute of Pharmaceutical Sciences, Federal University of Alagoas, Lourival Melo Mota Avenue, AC. Simões Campus, 57072-970, Alagoas, Maceió, Brazil
| | - Gabriel Felipe Silva Passos
- Laboratory of Medicinal Chemistry, Institute of Pharmaceutical Sciences, Federal University of Alagoas, Lourival Melo Mota Avenue, AC. Simões Campus, 57072-970, Alagoas, Maceió, Brazil
| | | | - Johnnatan Duarte de Freitas
- Department of Chemistry, Federal Institute of Alagoas, Maceió Campus, Mizael Domingues Street, 57020-600, Alagoas, Maceió, Brazil
| | - Grazielle Lobo Coelho
- Immunoregulation Research Group, Laboratory of Research in Virology and Immunology, Institute of Biological and Health Sciences, Lourival Melo Mota Avenue, AC. Simões Campus, 57072-970, Alagoas, Maceió, Brazil
| | - Júlia de Andrade Brandão
- Immunoregulation Research Group, Laboratory of Research in Virology and Immunology, Institute of Biological and Health Sciences, Lourival Melo Mota Avenue, AC. Simões Campus, 57072-970, Alagoas, Maceió, Brazil
| | - Leticia Anderson
- Immunoregulation Research Group, Laboratory of Research in Virology and Immunology, Institute of Biological and Health Sciences, Lourival Melo Mota Avenue, AC. Simões Campus, 57072-970, Alagoas, Maceió, Brazil; CESMAC University Center, 57051-160, Alagoas, Maceió, Brazil
| | - Ênio José Bassi
- Immunoregulation Research Group, Laboratory of Research in Virology and Immunology, Institute of Biological and Health Sciences, Lourival Melo Mota Avenue, AC. Simões Campus, 57072-970, Alagoas, Maceió, Brazil
| | - João Xavier de Araújo-Júnior
- Laboratory of Medicinal Chemistry, Institute of Pharmaceutical Sciences, Federal University of Alagoas, Lourival Melo Mota Avenue, AC. Simões Campus, 57072-970, Alagoas, Maceió, Brazil
| | - Shailly Tomar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, 247667, Uttarakhand, India
| | - Edeildo Ferreira da Silva-Júnior
- Laboratory of Medicinal Chemistry, Institute of Pharmaceutical Sciences, Federal University of Alagoas, Lourival Melo Mota Avenue, AC. Simões Campus, 57072-970, Alagoas, Maceió, Brazil; Biological and Molecular Chemistry Research Group, Institute of Chemistry and Biotechnology, Federal University of Alagoas, Lourival Melo Mota Avenue, AC. Simões Campus, 57072-970, Alagoas, Maceió, Brazil.
| |
Collapse
|
21
|
Pathak RK, Kim JM. Identification of histidine kinase inhibitors through screening of natural compounds to combat mastitis caused by Streptococcus agalactiae in dairy cattle. J Biol Eng 2023; 17:59. [PMID: 37752501 PMCID: PMC10523694 DOI: 10.1186/s13036-023-00378-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 09/18/2023] [Indexed: 09/28/2023] Open
Abstract
BACKGROUND Mastitis poses a major threat to dairy farms globally; it results in reduced milk production, increased treatment costs, untimely compromised genetic potential, animal deaths, and economic losses. Streptococcus agalactiae is a highly virulent bacteria that cause mastitis. The administration of antibiotics for the treatment of this infection is not advised due to concerns about the emergence of antibiotic resistance and potential adverse effects on human health. Thus, there is a critical need to identify new therapeutic approaches to combat mastitis. One promising target for the development of antibacterial therapies is the transmembrane histidine kinase of bacteria, which plays a key role in signal transduction pathways, secretion systems, virulence, and antibiotic resistance. RESULTS In this study, we aimed to identify novel natural compounds that can inhibit transmembrane histidine kinase. To achieve this goal, we conducted a virtual screening of 224,205 natural compounds, selecting the top ten based on their lowest binding energy and favorable protein-ligand interactions. Furthermore, molecular docking of eight selected antibiotics and five histidine kinase inhibitors with transmembrane histidine kinase was performed to evaluate the binding energy with respect to top-screened natural compounds. We also analyzed the ADMET properties of these compounds to assess their drug-likeness. The top two compounds (ZINC000085569031 and ZINC000257435291) and top-screened antibiotics (Tetracycline) that demonstrated a strong binding affinity were subjected to molecular dynamics simulations (100 ns), free energy landscape, and binding free energy calculations using the MM-PBSA method. CONCLUSION Our results suggest that the selected natural compounds have the potential to serve as effective inhibitors of transmembrane histidine kinase and can be utilized for the development of novel antibacterial veterinary medicine for mastitis after further validation through clinical studies.
Collapse
Affiliation(s)
- Rajesh Kumar Pathak
- Department of Animal Science and Technology, Chung-Ang University, Anseong-si, Gyeonggi-do, 17546, Republic of Korea
| | - Jun-Mo Kim
- Department of Animal Science and Technology, Chung-Ang University, Anseong-si, Gyeonggi-do, 17546, Republic of Korea.
| |
Collapse
|
22
|
Wang M, Zhang Z, Chen M, Lv Y, Tian S, Meng F, Zhang Y, Guo X, Chen Y, Yang M, Li J, Qiu T, Xu F, Li Z, Zhang Q, Yang J, Sun J, Zhang H, Zhang H, Li H, Wang W. FDW028, a novel FUT8 inhibitor, impels lysosomal proteolysis of B7-H3 via chaperone-mediated autophagy pathway and exhibits potent efficacy against metastatic colorectal cancer. Cell Death Dis 2023; 14:495. [PMID: 37537172 PMCID: PMC10400579 DOI: 10.1038/s41419-023-06027-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 07/18/2023] [Accepted: 07/27/2023] [Indexed: 08/05/2023]
Abstract
Metastatic colorectal cancer (mCRC) is a major cause of cancer-related mortality due to the absence of effective therapeutics. Thus, it is urgent to discover new drugs for mCRC. Fucosyltransferase 8 (FUT8) is a potential therapeutic target with high level in most malignant cancers including CRC. FUT8 mediates the core fucosylation of CD276 (B7-H3), a key immune checkpoint molecule (ICM), in CRC. FUT8-silence-induced defucosylation at N104 on B7-H3 attracts heat shock protein family A member 8 (HSPA8, also known as HSC70) to bind with 106-110 SLRLQ motif and consequently propels lysosomal proteolysis of B7-H3 through the chaperone-mediated autophagy (CMA) pathway. Then we report the development and characterization of a potent and highly selective small-molecule inhibitor of FUT8, named FDW028, which evidently prolongs the survival of mice with CRC pulmonary metastases (CRPM). FDW028 exhibits potent anti-tumor activity by defucosylation and impelling lysosomal degradation of B7-H3 through the CMA pathway. Taken together, FUT8 inhibition destabilizes B7-H3 through CMA-mediated lysosomal proteolysis, and FDW028 acts as a potent therapeutic candidate against mCRC by targeting FUT8. FDW028, an inhibitor specifically targeted FUT8, promotes defucosylation and consequent HSC70/LAMP2A-mediated lysosomal degradation of B7-H3, and exhibits potent anti-mCRC activities.
Collapse
Affiliation(s)
- Mengmeng Wang
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China
- Department of Pharmacy, The Second Affiliated Hospital of Soochow University, Soochow University, Suzhou, 215123, China
| | - Zhoudong Zhang
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China
| | - Mengxi Chen
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China
| | - Yixin Lv
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China
| | - Sheng Tian
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China
| | - Fanyi Meng
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China
| | - Yawen Zhang
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China
| | - Xuqin Guo
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China
| | - Yinshuang Chen
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China
| | - Man Yang
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China
| | - Jiawei Li
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China
| | - Tian Qiu
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China
| | - Fang Xu
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China
| | - Zhi Li
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China
| | - Qi Zhang
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China
| | - Jie Yang
- Institute of Medical Technology, Suzhou Vocational Health College, Suzhou, 215009, China
| | - Jing Sun
- Institute of Medical Technology, Suzhou Vocational Health College, Suzhou, 215009, China
| | - Hongjian Zhang
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China
| | - Haiyang Zhang
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China.
| | - Huanqiu Li
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China.
| | - Weipeng Wang
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China.
| |
Collapse
|
23
|
Shanker S, Sanner MF. Predicting Protein-Peptide Interactions: Benchmarking Deep Learning Techniques and a Comparison with Focused Docking. J Chem Inf Model 2023; 63:3158-3170. [PMID: 37167566 DOI: 10.1021/acs.jcim.3c00602] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The accurate prediction of protein structures achieved by deep learning (DL) methods is a significant milestone and has deeply impacted structural biology. Shortly after its release, AlphaFold2 has been evaluated for predicting protein-peptide interactions and shown to significantly outperform RoseTTAfold as well as a conventional blind docking method: PIPER-FlexPepDock. Since then, new AlphaFold2 models, trained specifically to predict multimeric assemblies, have been released and a new ab initio folding model OmegaFold has become available. Here, we assess docking success rates for these new DL folding models and compare their performance with our state-of-the-art, focused peptide-docking software AutoDock CrankPep (ADCP). The evaluation is done using the same dataset and performance metric for all methods. We show that, for a set of 99 nonredundant protein-peptide complexes, the new AlphaFold2 model outperforms other Deep Learning approaches and achieves remarkable docking success rates for peptides. While the docking success rate of ADCP is more modest when considering the top-ranking solution only, it samples correct solutions for around 62% of the complexes. Interestingly, different methods succeed on different complexes, and we describe a consensus docking approach using ADCP and AlphaFold2, which achieves a remarkable 60% for the top-ranking results and 66% for the top 5 results for this set of 99 protein-peptide complexes.
Collapse
Affiliation(s)
- Sudhanshu Shanker
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Michel F Sanner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| |
Collapse
|
24
|
Pathak RK, Kim WI, Kim JM. Targeting the PEDV 3CL protease for identification of small molecule inhibitors: an insight from virtual screening, ADMET prediction, molecular dynamics, free energy landscape, and binding energy calculations. J Biol Eng 2023; 17:29. [PMID: 37072787 PMCID: PMC10112315 DOI: 10.1186/s13036-023-00342-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 03/13/2023] [Indexed: 04/20/2023] Open
Abstract
BACKGROUND The porcine epidemic diarrhea virus (PEDV) represents a major health issue for piglets worldwide and does significant damage to the pork industry. Thus, new therapeutic approaches are urgently needed to manage PEDV infections. Due to the current lack of a reliable remedy, this present study aims to identify novel compounds that inhibit the 3CL protease of the virus involved in replication and pathogenesis. RESULTS To identify potent antiviral compounds against the 3CL protease, a virtual screening of natural compounds (n = 97,999) was conducted. The top 10 compounds were selected based on the lowest binding energy and the protein-ligand interaction analyzed. Further, the top five compounds that demonstrated a strong binding affinity were subjected to drug-likeness analysis using the ADMET prediction, which was followed by molecular dynamics simulations (500 ns), free energy landscape, and binding free energy calculations using the MM-PBSA method. Based on these parameters, four putative lead (ZINC38167083, ZINC09517223, ZINC04339983, and ZINC09517238) compounds were identified that represent potentially effective inhibitors of the 3CL protease. CONCLUSION Therefore, these can be utilized for the development of novel antiviral drugs against PEDV. However, this requires further validation through in vitro and in vivo studies.
Collapse
Affiliation(s)
- Rajesh Kumar Pathak
- Department of Animal Science and Technology, Chung-Ang University, Anseong-si, Gyeonggi-do 17546, Republic of Korea
| | - Won-Il Kim
- College of Veterinary Medicine, Jeonbuk National University, Iksan, Jeollabuk-do 54596, Republic of Korea
| | - Jun-Mo Kim
- Department of Animal Science and Technology, Chung-Ang University, Anseong-si, Gyeonggi-do 17546, Republic of Korea.
| |
Collapse
|
25
|
Peralta-Moreno MN, Anton-Muñoz V, Ortega-Alarcon D, Jimenez-Alesanco A, Vega S, Abian O, Velazquez-Campoy A, Thomson TM, Granadino-Roldán JM, Machicado C, Rubio-Martinez J. Autochthonous Peruvian Natural Plants as Potential SARS-CoV-2 M pro Main Protease Inhibitors. Pharmaceuticals (Basel) 2023; 16:ph16040585. [PMID: 37111342 PMCID: PMC10146424 DOI: 10.3390/ph16040585] [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: 03/02/2023] [Revised: 04/08/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023] Open
Abstract
Over 750 million cases of COVID-19, caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), have been reported since the onset of the global outbreak. The need for effective treatments has spurred intensive research for therapeutic agents based on pharmaceutical repositioning or natural products. In light of prior studies asserting the bioactivity of natural compounds of the autochthonous Peruvian flora, the present study focuses on the identification SARS-CoV-2 Mpro main protease dimer inhibitors. To this end, a target-based virtual screening was performed over a representative set of Peruvian flora-derived natural compounds. The best poses obtained from the ensemble molecular docking process were selected. These structures were subjected to extensive molecular dynamics steps for the computation of binding free energies along the trajectory and evaluation of the stability of the complexes. The compounds exhibiting the best free energy behaviors were selected for in vitro testing, confirming the inhibitory activity of Hyperoside against Mpro, with a Ki value lower than 20 µM, presumably through allosteric modulation.
Collapse
Affiliation(s)
- Maria Nuria Peralta-Moreno
- Department of Materials Science and Physical Chemistry, University of Barcelona, and the Institut de Recerca en Quimica Teorica i Computacional (IQTCUB), 08028 Barcelona, Spain
| | - Vanessa Anton-Muñoz
- Facultad de Farmacia y Bioquímica, Universidad Nacional Mayor de San Marcos, Jr. Puno 1002, Lima 15001, Peru
| | - David Ortega-Alarcon
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Ana Jimenez-Alesanco
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Sonia Vega
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain
| | - Olga Abian
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
- Instituto de Investigación Sanitaria de Aragón (IIS Aragon), 50009 Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas Digestivas (CIBERehd), 28029 Madrid, Spain
| | - Adrian Velazquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
- Instituto de Investigación Sanitaria de Aragón (IIS Aragon), 50009 Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas Digestivas (CIBERehd), 28029 Madrid, Spain
| | - Timothy M Thomson
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas Digestivas (CIBERehd), 28029 Madrid, Spain
- Institute of Molecular Biology of Barcelona (IBMB-CSIC), 08028 Barcelona, Spain
- Laboratorio de Investigación Traslacional y Biología Computacional, Facultad de Ciencias y Filosofía-LID, Universidad Peruana Cayetano Heredia, Av. Honorio Delgado 430, Lima 15102, Peru
| | - José Manuel Granadino-Roldán
- Departamento de Química Física y Analítica, Facultad de Ciencias Experimentales, Universidad de Jaén, Campus "Las Lagunillas" s/n, 23071 Jaén, Spain
| | - Claudia Machicado
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain
- Laboratorio de Investigación Traslacional y Biología Computacional, Facultad de Ciencias y Filosofía-LID, Universidad Peruana Cayetano Heredia, Av. Honorio Delgado 430, Lima 15102, Peru
| | - Jaime Rubio-Martinez
- Department of Materials Science and Physical Chemistry, University of Barcelona, and the Institut de Recerca en Quimica Teorica i Computacional (IQTCUB), 08028 Barcelona, Spain
| |
Collapse
|
26
|
Zhao J, Yu N, Zhao X, Quan W, Shu M. 3D-QSAR, molecular docking, and molecular dynamics analysis of dihydrodiazaindolone derivatives as PARP-1 inhibitors. J Mol Model 2023; 29:131. [PMID: 37020092 DOI: 10.1007/s00894-023-05525-4] [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: 09/16/2022] [Accepted: 03/21/2023] [Indexed: 04/07/2023]
Abstract
CONTEXT PARP-1 plays an important role in DNA repair and apoptosis, and PARP-1 inhibitors have shown to be effective in the treatment of several malignancies. To evaluate the function of new PARP-1 inhibitors as anticancer adjuvant medicines, 3D-QSAR, molecular docking, and molecular dynamics (MD) simulations of a sequence of dihydrodiazepinoindolone derivatives PARP-1 inhibitors were undertaken in this study. METHODS In this paper, 43 PARP-1 inhibitors were studied in a three-dimensional quantitative structure-activity relationship (3D-QSAR) using comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA). CoMFA with q2 of 0.675 and r2 of 0.981 was achieved, as was CoMSIA with q2 of 0.755 and r2 of 0.992. The changed areas of these compounds are shown by steric, electrostatic, hydrophobic, and hydrogen-bonded acceptor field contour maps. Subsequently, molecular docking, and molecular dynamics simulations further confirmed that key residues Gly863 and Ser904 of PARP-1 are vital residues for protein interactions and their binding affinity. The effects of 3D-QSAR, molecular docking and molecular dynamics simulations supply a new route for the search of new PARP-1 inhibitors. Finally, we designed eight new compounds with exact activity and ADME/T properties.
Collapse
Affiliation(s)
- Jing Zhao
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 400054, China
| | - Na Yu
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 400054, China
| | - Xuemin Zhao
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 400054, China
| | - Wenxuan Quan
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 400054, China
| | - Mao Shu
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 400054, China.
| |
Collapse
|
27
|
Biswas S, Mita MA, Afrose S, Hasan MR, Islam MT, Rahman MA, Ara MJ, Chowdhury MBA, Meem HN, Mamunuzzaman M, Ahammad T, Ashik IU, Ibrahim MM, Imam MT, Hossain MA, Saleh MA. Integrated Computational Approaches for Inhibiting Sex Hormone-Binding Globulin in Male Infertility by Screening Potent Phytochemicals. Life (Basel) 2023; 13:476. [PMID: 36836833 PMCID: PMC9966787 DOI: 10.3390/life13020476] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 01/01/2023] [Accepted: 01/18/2023] [Indexed: 02/11/2023] Open
Abstract
Male infertility is significantly influenced by the plasma-protein sex hormone-binding globulin (SHBG). Male infertility, erectile dysfunction, prostate cancer, and several other male reproductive system diseases are all caused by reduced testosterone bioavailability due to its binding to SHBG. In this study, we have identified 345 phytochemicals from 200 literature reviews that potentially inhibit severe acute respiratory syndrome coronavirus 2. Only a few studies have been done using the SARS-CoV-2 inhibitors to identify the SHBG inhibitor, which is thought to be the main protein responsible for male infertility. In virtual-screening and molecular-docking experiments, cryptomisrine, dorsilurin E, and isoiguesterin were identified as potential SHBG inhibitors with binding affinities of -9.2, -9.0, and -8.8 kcal/mol, respectively. They were also found to have higher binding affinities than the control drug anastrozole (-7.0 kcal/mol). In addition to favorable pharmacological properties, these top three phytochemicals showed no adverse effects in pharmacokinetic evaluations. Several molecular dynamics simulation profiles' root-mean-square deviation, radius of gyration, root-mean-square fluctuation, hydrogen bonds, and solvent-accessible surface area supported the top three protein-ligand complexes' better firmness and stability than the control drug throughout the 100 ns simulation period. These combinatorial drug-design approaches indicate that these three phytochemicals could be developed as potential drugs to treat male infertility.
Collapse
Affiliation(s)
- Suvro Biswas
- Miocrobiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Mohasana Akter Mita
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Shamima Afrose
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Md. Robiul Hasan
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Md. Tarikul Islam
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Md. Ashiqur Rahman
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Mst. Jasmin Ara
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | | | - Habibatun Naher Meem
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Md. Mamunuzzaman
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Tanvir Ahammad
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Istiaq Uddin Ashik
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Munjed M. Ibrahim
- Department of Pharmaceutical Chemistry, College of Pharmacy, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Mohammad Tarique Imam
- Department of Clinical Pharmacy, College of Pharmacy, Prince Sattam Bin Abdul Aziz University, Al Kharj, Pin 11942, Saudi Arabia
| | - Mohammad Akbar Hossain
- Department of Pharmacology and Toxicology, Faculty of Medicine in Al-Qunfudah, Umm Al-Qura University, Makkah 28814, Saudi Arabia
| | - Md. Abu Saleh
- Miocrobiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| |
Collapse
|
28
|
Approaching the Dimerization Mechanism of Small Molecule Inhibitors Targeting PD-L1 with Molecular Simulation. Int J Mol Sci 2023; 24:ijms24021280. [PMID: 36674800 PMCID: PMC9866166 DOI: 10.3390/ijms24021280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/04/2023] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
Abstract
Inhibitors blocking the PD-1/PD-L1 immune checkpoint demonstrate impressive anti-tumor immunity, and small molecule inhibitors disclosed by the Bristol-Myers Squibb (BMS) company have become a hot topic. In this work, by modifying the carbonyl group of BMS-202 into a hydroxyl group to achieve two enantiomers (MS and MR) with a chiral center, we found that this is an effective way to regulate its hydrophobicity and thus to reduce the negative effect of polar solvation free energy, which enhances the stability of PD-L1 dimer/inhibitor complexes. Moreover, we studied the binding modes of BMS-200 and BMS-202-related small molecule inhibitors by molecular dynamics simulation to explore their inhibitory mechanism targeting PD-L1 dimerization. The results showed that the size exclusion effect of the inhibitors triggered the rearrangement of the residue ATyr56, leading to the formation of an axisymmetric tunnel-shaped pocket, which is an important structural basis for improving the binding affinity of symmetric inhibitors with PD-L1. Furthermore, after inhibitor dissociation, the conformation of ATyr123 and BMet115 rearranged, which blocked the entrance of the binding pocket, while the reverse rearrangements of the same residues occurred when the PD-L1 monomer was complexed with the inhibitors, preparing PD-L1 for dimerization. Overall, this study casts a new light on the inhibitory mechanism of BMS inhibitors targeting PD-L1 dimerization and provides an idea for designing novel small molecule inhibitors for future cancer immunotherapy.
Collapse
|
29
|
Li Z, Wu C, Li Y, Liu R, Lu K, Wang R, Liu J, Gong C, Yang C, Wang X, Zhan CG, Luo HB. Free energy perturbation-based large-scale virtual screening for effective drug discovery against COVID-19. THE INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS 2023; 37:45-57. [PMID: 38603271 PMCID: PMC9396747 DOI: 10.1177/10943420221117797] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
As a theoretically rigorous and accurate method, FEP-ABFE (Free Energy Perturbation-Absolute Binding Free Energy) calculations showed great potential in drug discovery, but its practical application was difficult due to high computational cost. To rapidly discover antiviral drugs targeting SARS-CoV-2 Mpro and TMPRSS2, we performed FEP-ABFE-based virtual screening for ∼12,000 protein-ligand binding systems on a new generation of Tianhe supercomputer. A task management tool was specifically developed for automating the whole process involving more than 500,000 MD tasks. In further experimental validation, 50 out of 98 tested compounds showed significant inhibitory activity towards Mpro, and one representative inhibitor, dipyridamole, showed remarkable outcomes in subsequent clinical trials. This work not only demonstrates the potential of FEP-ABFE in drug discovery but also provides an excellent starting point for further development of anti-SARS-CoV-2 drugs. Besides, ∼500 TB of data generated in this work will also accelerate the further development of FEP-related methods.
Collapse
Affiliation(s)
- Zhe Li
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, P. R. China
| | - Chengkun Wu
- State Key Laboratory of High Performance Computing, Changsha, P. R. China
| | - Yishui Li
- State Key Laboratory of High Performance Computing, Changsha, P. R. China
| | - Runduo Liu
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, P. R. China
| | - Kai Lu
- State Key Laboratory of High Performance Computing, Changsha, P. R. China
| | - Ruibo Wang
- State Key Laboratory of High Performance Computing, Changsha, P. R. China
| | - Jie Liu
- State Key Laboratory of High Performance Computing, Changsha, P. R. China
| | - Chunye Gong
- State Key Laboratory of High Performance Computing, Changsha, P. R. China
| | - Canqun Yang
- National Supercomputer Center in Tianjin, Tianjin, P. R. China
| | - Xin Wang
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, P. R. China
- Marine Biomedical Research Institute of Qingdao, Qingdao, P. R. China
| | - Chang-Guo Zhan
- Molecular Modeling and Biopharmaceutical Center, College of Pharmacy, University of Kentucky, Lexington, KY, USA
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA
| | - Hai-Bin Luo
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, P. R. China
- School of Pharmaceutical Sciences, Hainan University, Haikou, P. R. China
| |
Collapse
|
30
|
Alrouji M, Majrashi TA, Alhumaydhi FA, Zari A, Zari TA, Al Abdulmonem W, Sharaf SE, Shahwan M, Anwar S, Shamsi A, Atiya A. Unveiling Phytoconstituents with Inhibitory Potential Against Tyrosine-Protein Kinase Fyn: A Comprehensive Virtual Screening Approach Targeting Alzheimer's Disease. J Alzheimers Dis 2023; 96:827-844. [PMID: 37899058 DOI: 10.3233/jad-230828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2023]
Abstract
BACKGROUND Tyrosine-protein kinase Fyn (Fyn) is a critical signaling molecule involved in various cellular processes, including neuronal development, synaptic plasticity, and disease pathogenesis. Dysregulation of Fyn kinase has been implicated in various complex diseases, including neurodegenerative disorders such as Alzheimer's and Parkinson's diseases, as well as different cancer types. Therefore, identifying small molecule inhibitors that can inhibit Fyn activity holds substantial significance in drug discovery. OBJECTIVE The aim of this study was to identify potential small-molecule inhibitors among bioactive phytoconstituents against tyrosine-protein kinase Fyn. METHODS Through a comprehensive approach involving molecular docking, drug likeliness filters, and molecular dynamics (MD) simulations, we performed a virtual screening of a natural compounds library. This methodology aimed to pinpoint compounds potentially interacting with Fyn kinase and inhibiting its activity. RESULTS This study finds two potential natural compounds: Dehydromillettone and Tanshinone B. These compoundsdemonstrated substantial affinity and specific interactions towards the Fyn binding pocket. Their conformations exhibitedcompatibility and stability, indicating the formation of robust protein-ligand complexes. A significant array of non-covalentinteractions supported the structural integrity of these complexes. CONCLUSION Dehydromillettone and Tanshinone B emerge as promising candidates, poised for further optimization as Fynkinase inhibitors with therapeutic applications. In a broader context, this study demonstrates the potential of computationaldrug discovery, underscoring its utility in identifying compounds with clinical significance. The identified inhibitors holdpromise in addressing a spectrum of cancer and neurodegenerative disorders. However, their efficacy and safety necessitatevalidation through subsequent experimental studies.
Collapse
Affiliation(s)
- Mohammed Alrouji
- Department of Medical Laboratories, College of Applied Medical Sciences, Shaqra University, Shaqra, Saudi Arabia
| | - Taghreed A Majrashi
- Department of Pharmacognosy, College of Pharmacy, King Khalid University (KKU), Guraiger, Abha, Saudi Arabia
| | - Fahad A Alhumaydhi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Ali Zari
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Princess Dr. Najla Bint Saud Al-Saud Center for Excellence Research in Biotechnology, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Talal A Zari
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Waleed Al Abdulmonem
- Department of Pathology, College of Medicine, Qassim University, Buraydah, Saudi Arabia
| | - Sharaf E Sharaf
- Pharmaceutical Chemistry Department, College of Pharmacy Umm Al-Qura University Makkah, Saudi Arabia
| | - Moyad Shahwan
- Center for Medical and Bio-Allied Health Sciences, Ajman University, Ajman, UAE
| | - Saleha Anwar
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, India
| | - Anas Shamsi
- Center for Medical and Bio-Allied Health Sciences, Ajman University, Ajman, UAE
| | - Akhtar Atiya
- Department of Pharmacognosy, College of Pharmacy, King Khalid University (KKU), Guraiger, Abha, Saudi Arabia
| |
Collapse
|
31
|
Elseginy SA. Virtual screening and structure-based 3D pharmacophore approach to identify small-molecule inhibitors of SARS-CoV-2 M pro. J Biomol Struct Dyn 2022; 40:13658-13674. [PMID: 34676801 DOI: 10.1080/07391102.2021.1993341] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The outbreak caused by a coronavirus 2 has required quick and potential treatment strategies. The main protease enzyme Mpro plays an important role in the viral replication which renders it an important target for discovering SARS-CoV-2 inhibitors. In this study, 3D pharmacophore structure-based virtual screening and molecular docking were conducted using MOE and Bristol University Docking Engine (BUDE). Around 400,000 molecules of ZINC15 database were docked against the crystal structure of main protease, followed by 3D pharmacophore filtration. Six top-ranked hits (ZINC58717986, ZINC60399606, ZINC58662884, ZINC45988635, ZINC54706757 and ZINC17320595) were identified based on their strong spatial affinity and forming H-bonds with key residues H41, E166, Q189 and T190 of the binding pocket of Mpro SARS-CoV-2. The 6 hits subjected to molecular dynamics simulations for 100 ns followed by binding free energy calculations using MM-PBSA technique. Interestingly, three hits showed free binding energy (ΔGbinding) lower than tert-butyl N-[1-[(2S)-1-[[(2S)-4-(benzylamino)-3,4-dioxo-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl]amino]-3-cyclopropyl-1-oxopropan-2-yl]-2-oxopyridin-3-yl]carbamate (α-ketoamide 13 b) (ΔGbinding) -76.67 ± 0.5 kJ/mol which suggested their potential against SARS-CoV-2. The best binding free energy candidates, ZINC58717986 (ΔGbinding) -98.41 ± 0.7 kJ/mol. The second-best hit candidate, ZINC54706757 (ΔGbinding) -83.4 ± 0.6 kJ/mol and the third one ZINC17320595 (ΔGbinding) -78.85 ± 0.5 kJ/mol. Per residue decomposition free energy indicates H41, S46, H164, E166, D187, Q189 and Q192 are hot spot residues while residues M49, M165, L167 and P168 contribute to the hydrophobic interactions. The pharmacokinetic study suggests that the selected 6 hits possess drug-like properties. The 3D pharmacophore virtual screening, molecular dynamics and MM-PBSA approaches facilitated identification 3 promising hits with low free binding energy as SARS-CoV-2 inhibitors.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Samia A Elseginy
- Molecular Modelling Lab., Biochemistry School, Bristol University, Bristol, UK.,Green Chemistry Department, Chemical Industries Research Division, National Research Centre, Egypt
| |
Collapse
|
32
|
Bhadane R, Salo-Ahen OMH. High-Throughput Molecular Dynamics-Based Alchemical Free Energy Calculations for Predicting the Binding Free Energy Change Associated with the Selected Omicron Mutations in the Spike Receptor-Binding Domain of SARS-CoV-2. Biomedicines 2022; 10:2779. [PMID: 36359299 PMCID: PMC9687918 DOI: 10.3390/biomedicines10112779] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/17/2022] [Accepted: 10/25/2022] [Indexed: 11/10/2023] Open
Abstract
The ongoing pandemic caused by SARS-CoV-2 has gone through various phases. Since the initial outbreak, the virus has mutated several times, with some lineages showing even stronger infectivity and faster spread than the original virus. Among all the variants, omicron is currently classified as a variant of concern (VOC) by the World Health Organization, as the previously circulating variants have been replaced by it. In this work, we have focused on the mutations observed in omicron sub lineages BA.1, BA.2, BA.4 and BA.5, particularly at the receptor-binding domain (RBD) of the spike protein that is responsible for the interactions with the host ACE2 receptor and binding of antibodies. Studying such mutations is particularly important for understanding the viral infectivity, spread of the disease and for tracking the escape routes of this virus from antibodies. Molecular dynamics (MD) based alchemical free energy calculations have been shown to be very accurate in predicting the free energy change, due to a mutation that could have a deleterious or a stabilizing effect on either the protein itself or its binding affinity to another protein. Here, we investigated the significance of five spike RBD mutations on the stability of the spike protein binding to ACE2 by free energy calculations using high throughput MD simulations. For comparison, we also used conventional MD simulations combined with a Molecular Mechanics-Generalized Born Surface Area (MM-GBSA) based approach, and compared our results with the available experimental data. Overall, the alchemical free energy calculations performed far better than the MM-GBSA approach in predicting the individual impact of the mutations. When considering the experimental variation, the alchemical free energy method was able to produce a relatively accurate prediction for N501Y, the mutant that has previously been reported to increase the binding affinity to hACE2. On the other hand, the other individual mutations seem not to have a significant effect on the spike RBD binding affinity towards hACE2.
Collapse
Affiliation(s)
- Rajendra Bhadane
- Structural Bioinformatics Laboratory, Faculty of Science and Engineering, Biochemistry, Åbo Akademi University, FI-20520 Turku, Finland
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Pharmacy, Åbo Akademi University, FI-20520 Turku, Finland
| | - Outi M. H. Salo-Ahen
- Structural Bioinformatics Laboratory, Faculty of Science and Engineering, Biochemistry, Åbo Akademi University, FI-20520 Turku, Finland
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Pharmacy, Åbo Akademi University, FI-20520 Turku, Finland
| |
Collapse
|
33
|
Lin HYJ, Battaje RR, Tan J, Doddareddy M, Dhaked HPS, Srivastava S, Hawkins BA, Al-Shdifat LMH, Hibbs DE, Panda D, Groundwater PW. Discovery of 2',6-Bis(4-hydroxybenzyl)-2-acetylcyclohexanone, a Novel FtsZ Inhibitor. Molecules 2022; 27:6993. [PMID: 36296585 PMCID: PMC9610434 DOI: 10.3390/molecules27206993] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 10/13/2022] [Accepted: 10/13/2022] [Indexed: 03/04/2024] Open
Abstract
Multi-drug resistance is increasing in the pathogenic bacterium S. pneumoniae, which is mainly responsible for meningitis and community-acquired pneumonia (CAP), highlighting the need for new anti-pneumococcal agents. We have identified a potential anti-pneumococcal agent, enol 3, which acts by hindering the cell division process by perturbing Z-ring dynamics inside the cell. Enol 3 was also shown to inhibit FtsZ polymerization and induce its aggregation in vitro but does not affect the activity of tubulin and alkaline phosphatase. Docking studies show that 3 binds near the T7 loop, which is the catalytic site of FtsZ. Similar effects on Z-ring and FtsZ assembly were observed in B. subtilis, indicating that 3 could be a broad-spectrum anti-bacterial agent useful in targeting Gram-positive bacteria. In conclusion, compound 3 shows strong anti-pneumococcal activity, prompting further pre-clinical studies to explore its potential.
Collapse
Affiliation(s)
- Hsuan-Yu J. Lin
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Rachana Rao Battaje
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Jinlong Tan
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Munikumar Doddareddy
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Hemendra Pal Singh Dhaked
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Shalini Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Bryson A. Hawkins
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | | | - David E. Hibbs
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Dulal Panda
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
- National Institute of Pharmaceutical Education and Research, Nagar 160062, India
| | - Paul W. Groundwater
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| |
Collapse
|
34
|
Mishra RP, Gupta S, Rathore AS, Goel G. Multi-Level High-Throughput Screening for Discovery of Ligands That Inhibit Insulin Aggregation. Mol Pharm 2022; 19:3770-3783. [PMID: 36173709 DOI: 10.1021/acs.molpharmaceut.2c00219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have developed a multi-level virtual screening protocol to identify lead molecules from the FDA inactives database that can inhibit insulin aggregation. The method is based on the presence of structural and interaction specificity in non-native aggregation pathway protein-protein interactions. Some key challenges specific to the present problem, when compared with native protein association, include structural heterogeneity of the protein species involved, multiple association pathways, and relatively higher probability of conformational rearrangement of the association complex. In this multi-step method, the inactives database was first screened using the dominant pharmacophore features of previously identified molecules shown to significantly inhibit insulin aggregation nucleation by binding to its aggregation-prone conformers. We then performed ensemble docking of several low-energy ligand conformations on these aggregation-prone conformers followed by molecular dynamics simulations and binding affinity calculations on a subset of docked complexes to identify a final set of five potential lead molecules to inhibit insulin aggregation nucleation. Their effect on aggregation inhibition was extensively investigated by incubating insulin under aggregation-prone aqueous buffer conditions (low pH, high temperature). Aggregation kinetics were characterized using size exclusion chromatography and Thioflavin T fluorescence assay, and the secondary structure was determined using circular dichroism spectroscopy. Riboflavin provided the best aggregation inhibition, with 85% native monomer retention after 48 h incubation under aggregation-prone conditions, whereas the no-ligand formulation showed complete monomer loss after 36 h. Further, insulin incubated with two of the screened inactives (aspartame, riboflavin) had the characteristic α-helical dip in CD spectra, while the no-ligand formulation showed a change to β-sheet rich conformations.
Collapse
Affiliation(s)
- Rit Pratik Mishra
- Department of Chemical Engineering, Indian Institute Technology Delhi, New Delhi, 110016, India
| | - Surbhi Gupta
- Department of Chemical Engineering, Indian Institute Technology Delhi, New Delhi, 110016, India
| | - Anurag Singh Rathore
- Department of Chemical Engineering, Indian Institute Technology Delhi, New Delhi, 110016, India
| | - Gaurav Goel
- Department of Chemical Engineering, Indian Institute Technology Delhi, New Delhi, 110016, India
| |
Collapse
|
35
|
Characterizing aripiprazole and its ester derivatives, lauroxil and cavoxil, in interaction with dopamine D2 receptor: Molecular docking and dynamics simulations with physicochemical appraisals. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
36
|
Jain M, Anand A, Shah A. Exploring the Potential Role of Theaflavin-3,3′-Digallate in Inhibiting Various Stages of SARS-CoV-2 Life Cycle: An In-Silico Approach. CHEMISTRY AFRICA 2022. [PMCID: PMC9219385 DOI: 10.1007/s42250-022-00376-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Introduction Theaflavins belong to the class of polyphenols that are predominantly found in black tea. The major derivatives of theaflavins found in black tea are theaflavin (TF1), theaflavin-3-gallate (TF2A), theaflavin-3′-gallate (TF2B), and theaflavin-3,3′-digallate (TF3). Theaflavin-3,3′-digallate (TF3) is a natural compound present in black tea and known to possess antiviral activity. This study had attempted to explore the potential role of TF3 in inhibiting various stages of the SARS-CoV-2 life cycle. Methods Molecular docking studies of TF3 along with positive controls was performed on eight different targets of SARS-CoV-2 followed by binding free energy (MM-GBSA) calculations. The docked complexes with favourable docking and binding free energy results were subjected to molecular dynamics (MD) simulation studies to assess the stability of the dock complex. Finally, TF3 and all the positive controls were taken for ADMET analysis. Results The docking and binding free energy results of TF3 was compared against the positive controls. TF3 showed the highest binding energy against all the targets and formed more stable interactions for a longer duration on MD simulations with CLpro, RdRp, helicase and spike protein. Also, the promising in-silico ADMET profile further warrants the exploration of this compound through in-vitro and in-vivo methods. Conclusion Through this study, we tried to evaluate the role of theaflavin-3,3’-digallate on multiple targets of SARS-CoV-2, and the positive in-silico results which were obtained on various pharmacodynamic and pharmacokinetic parameters, give a ray of hope as a potential therapeutic drug to this rapidly spreading disease. The search for a curative therapy for SARS-CoV-2 is still ongoing. The favourable preliminary results of TF3 through in-silico analysis offers a ray of hope in ending this devasting pandemic. Supplementary Information The online version contains supplementary material available at 10.1007/s42250-022-00376-7.
Collapse
Affiliation(s)
- Manav Jain
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, Punjab India
| | - Aishwarya Anand
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, Punjab India
| | - Ashish Shah
- Department of Pharmacy, Sumandeep Vidyapeeth, Vadodara, Gujarat India
| |
Collapse
|
37
|
Mechanism of a Herbal Formula Associated with Prognosis and Immune Infiltration in LIHC: Transcriptomics Analysis and Molecular Dynamics Simulations. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:6084321. [PMID: 35754689 PMCID: PMC9217603 DOI: 10.1155/2022/6084321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/08/2022] [Accepted: 05/19/2022] [Indexed: 11/26/2022]
Abstract
Background The aim of this study is to explore the interactions between effective monomers of herbal formulas and their therapeutic targets using systems biology approaches which may be a promising approach to unraveling their underlying mechanisms. Shentao Ruangan decoction (STRGD), which has been experimentally, clinically demonstrated to be effective in treating liver hepatocellular carcinoma (LIHC), was selected. Methods Bioactive ingredients and drug targets of STRGD were retrieved from the traditional Chinese medicine systems pharmacology database and analysis platform and BATMAN-TCM databases. LIHC-related differentially expressed genes (DEGs) and key modules were identified by a weighted gene coexpression network analysis using The Cancer Genome Atlas data. The Kaplan–Meier analysis was used to investigate the relationship between STRGD tumor targets and patients survival. The CIBERSORT deconvolution algorithm was used to analyze the correlation between STRGD tumor targets and infiltrating immune cells. Enrichment analysis was used to analyze biological functions. Interactions between STRGD compounds and LIHC-immune-related genes were investigated using molecular docking and MDS. Results We identified 24 STRGD tumor targets, which were found to be correlated with survival and the level of immune cell infiltration in LIHC patients. Immune infiltration, gene set enrichment, and Kyoto Encyclopedia of Genes and Genomes analyses highlighted the roles of T and B cell subsets, which were both related to activator protein 1 (AP1), in STRGD action. Docking studies and HPLC indicated that tanshinone IIA is the main compound of STRGD in LIHC treatment, and MDS showed that the potential LIHC-immune-related targets 1FOS and 1JUN firmly bind to tanshinone IIA. Conclusions The mechanisms of STRGD in improving the immune and survival status of LIHC patients include interactions between STRGD compounds and LIHC-immune-related targets. The findings of this study can guide research studies on the potential usefulness of tanshinone IIA in the development of drugs targeting 1JUN and 1FOS for the treatment of LIHC.
Collapse
|
38
|
Peters XQ, Agoni C, Soliman MES. Unravelling the Structural Mechanism of Action of 5-methyl-5-[4-(4-oxo-3H-quinazolin-2-yl)phenyl]imidazolidine-2,4-dione in Dual-Targeting Tankyrase 1 and 2: A Novel Avenue in Cancer Therapy. Cell Biochem Biophys 2022; 80:505-518. [PMID: 35637423 DOI: 10.1007/s12013-022-01076-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 05/21/2022] [Indexed: 11/03/2022]
Abstract
Tankyrase (TNKS) belonging to the poly(ADPribose) polymerase family, are known for their multi-functioning capabilities, and play an essential role in the Wnt β-catenin pathway and various other cellular processes. Although showing inhibitory potential at a nanomolar level, the structural dual-inhibitory mechanism of the novel TNKS inhibitor, 5-methyl-5-[4-(4-oxo-3H-quinazolin-2-yl)phenyl]imidazolidine-2,4-dione, remains unexplored. By employing advanced molecular modeling, this study provides these insights. Results of sequence alignments of binding site residues identified conserved residues; GLY1185 and ILE1224 in TNKS-1 and PHE1035 and PRO1034 in TNKS-2 as crucial mediators of the dual binding mechanism of 5-methyl-5-[4-(4-oxo-3H-quinazolin-2-yl)phenyl]imidazolidine-2,4-dione, corroborated by high per-residue energy contributions and consistent high-affinity interactions of these residues. Estimation of the binding free energy of 5-methyl-5-[4-(4-oxo-3H-quinazolin-2-yl)phenyl]imidazolidine-2,4-dione showed estimated total energy of -43.88 kcal/mol and -30.79 kcal/mol towards TNKS-1 and 2, respectively, indicating favorable analogous dual binding as previously reported. Assessment of the conformational dynamics of TNKS-1 and 2 upon the binding of 5-methyl-5-[4-(4-oxo-3H-quinazolin-2-yl)phenyl]imidazolidine-2,4-dione revealed similar structural changes characterized by increased flexibility and solvent assessible surface area of the residues inferring an analogous structural binding mechanism. Insights from this study show that peculiar, conserved residues are the driving force behind the dual inhibitory mechanism of 5-methyl-5-[4-(4-oxo-3H-quinazolin-2-yl)phenyl]imidazolidine-2,4-dione and could aid in the design of novel dual inhibitors of TNKS-1 and 2 with improved therapeutic properties.
Collapse
Affiliation(s)
- Xylia Q Peters
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Clement Agoni
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa.,West African Centre for Computational Analysis, Accra, Ghana
| | - Mahmoud E S Soliman
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa.
| |
Collapse
|
39
|
Jamir E, Sarma H, Priyadarsinee L, Nagamani S, Kiewhuo K, Gaur AS, Rawal RK, Murugan NA, Subramanian V, Sastry GN. Applying polypharmacology approach for drug repurposing for SARS-CoV2. J CHEM SCI 2022; 134:57. [PMID: 35498548 PMCID: PMC9028909 DOI: 10.1007/s12039-022-02046-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/15/2022] [Accepted: 02/17/2022] [Indexed: 02/06/2023]
Abstract
Exploring the new therapeutic indications of known drugs for treating COVID-19, popularly known as drug repurposing, is emerging as a pragmatic approach especially owing to the mounting pressure to control the pandemic. Targeting multiple targets with a single drug by employing drug repurposing known as the polypharmacology approach may be an optimised strategy for the development of effective therapeutics. In this study, virtual screening has been carried out on seven popular SARS-CoV-2 targets (3CLpro, PLpro, RdRp (NSP12), NSP13, NSP14, NSP15, and NSP16). A total of 4015 approved drugs were screened against these targets. Four drugs namely venetoclax, tirilazad, acetyldigitoxin, and ledipasvir have been selected based on the docking score, ability to interact with four or more targets and having a reasonably good number of interactions with key residues in the targets. The MD simulations and MM-PBSA studies showed reasonable stability of protein-drug complexes and sustainability of key interactions between the drugs with their respective targets throughout the course of MD simulations. The identified four drug molecules were also compared with the known drugs namely elbasvir and nafamostat. While the study has provided a detailed account of the chosen protein-drug complexes, it has explored the nature of seven important targets of SARS-CoV-2 by evaluating the protein-drug complexation process in great detail.
Collapse
Affiliation(s)
- Esther Jamir
- Advanced Computation and Data Sciences Division, CSIR – North East Institute of Science and Technology, Jorhat, Assam 785006 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Himakshi Sarma
- Advanced Computation and Data Sciences Division, CSIR – North East Institute of Science and Technology, Jorhat, Assam 785006 India
| | - Lipsa Priyadarsinee
- Advanced Computation and Data Sciences Division, CSIR – North East Institute of Science and Technology, Jorhat, Assam 785006 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Selvaraman Nagamani
- Advanced Computation and Data Sciences Division, CSIR – North East Institute of Science and Technology, Jorhat, Assam 785006 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Kikrusenuo Kiewhuo
- Advanced Computation and Data Sciences Division, CSIR – North East Institute of Science and Technology, Jorhat, Assam 785006 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Anamika Singh Gaur
- Advanced Computation and Data Sciences Division, CSIR – North East Institute of Science and Technology, Jorhat, Assam 785006 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Ravindra K Rawal
- Advanced Computation and Data Sciences Division, CSIR – North East Institute of Science and Technology, Jorhat, Assam 785006 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Natarajan Arul Murugan
- Department of Computer Science, School of Electrical Engineering and Computer Science, KTH Royal Institute of Technology, 106 91 Stockholm, Sweden
| | - Venkatesan Subramanian
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- Center for High Computing, CSIR- Central Leather Research Institute (CLRI), Chennai, India
| | - G Narahari Sastry
- Advanced Computation and Data Sciences Division, CSIR – North East Institute of Science and Technology, Jorhat, Assam 785006 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| |
Collapse
|
40
|
Liao J, Nie X, Unarta IC, Ericksen SS, Tang W. In Silico Modeling and Scoring of PROTAC-Mediated Ternary Complex Poses. J Med Chem 2022; 65:6116-6132. [PMID: 35412837 DOI: 10.1021/acs.jmedchem.1c02155] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proteolysis targeting chimeras (PROTACs) are molecules that induce protein degradation via formation of ternary complexes between an E3 ubiquitin ligase and a target protein. The rational design of PROTACs requires accurate knowledge of the native configuration of the PROTAC-induced ternary complex. This study demonstrates that native and non-native ternary complex poses can be distinguished based on the pose occupancy time in MD, where native poses exhibit longer occupancy times at both room and higher temperatures. Candidate poses are generated by MD sampling and pre-ranked by classic MM/GBSA. A specific heating scheme is then applied to accelerate ternary pose departure, with the pose occupancy time and fraction being measured. This scoring identifies the native pose in all systems tested. Its success is partially attributed to the dynamic nature of pose departure analyses, which accounts for entropic effects typically neglected in the faster static scoring methods, while entropy plays a greater role in protein-protein than in protein-ligand systems.
Collapse
Affiliation(s)
- Junzhuo Liao
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Xueqing Nie
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Ilona Christy Unarta
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Spencer S Ericksen
- Drug Development Core, UW Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Weiping Tang
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.,Drug Development Core, UW Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| |
Collapse
|
41
|
Pathak RK, Seo YJ, Kim JM. Structural insights into inhibition of PRRSV Nsp4 revealed by structure-based virtual screening, molecular dynamics, and MM-PBSA studies. J Biol Eng 2022; 16:4. [PMID: 35193698 PMCID: PMC8864930 DOI: 10.1186/s13036-022-00284-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 02/02/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Porcine reproductive and respiratory syndrome respiratory sickness in weaned and growing pigs, as well as sow reproductive failure, and its infection is regarded as one of the most serious swine illnesses worldwide. Given the current lack of an effective treatment, in this study, we identified natural compounds capable of inhibiting non-structural protein 4 (Nsp4) of the virus, which is involved in their replication and pathogenesis. RESULTS We screened natural compounds (n = 97,999) obtained from the ZINC database against Nsp4 and selected the top 10 compounds for analysing protein-ligand interactions and physicochemical properties. The five compounds demonstrating strong binding affinity were then subjected to molecular dynamics simulations (100 ns) and binding free energy calculations. Based on analysis, we identified four possible lead compounds that represent potentially effective drug-like inhibitors. CONCLUSIONS These methods identified that these natural compounds are capable of inhibiting Nsp4 and possibly effective as antiviral therapeutics against PRRSV.
Collapse
Affiliation(s)
- Rajesh Kumar Pathak
- Department of Animal Science and Technology, Chung-Ang University, Anseong-si, Gyeonggi-do, 17546, Republic of Korea
| | - Young-Jun Seo
- Department of Animal Science and Technology, Chung-Ang University, Anseong-si, Gyeonggi-do, 17546, Republic of Korea
| | - Jun-Mo Kim
- Department of Animal Science and Technology, Chung-Ang University, Anseong-si, Gyeonggi-do, 17546, Republic of Korea.
| |
Collapse
|
42
|
Kankariya RA, Chaudhari AB, Dandi ND. Inhibitory efficacy of 2, 4-diacetylphloroglucinol against SARS-COV-2 proteins: in silico study. Biologia (Bratisl) 2022; 77:815-828. [PMID: 35125499 PMCID: PMC8800849 DOI: 10.1007/s11756-021-00979-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 11/24/2021] [Indexed: 11/29/2022]
Affiliation(s)
- Raksha A. Kankariya
- School of Life Sciences, Kavayitri Bahinabai Chaudhari North Maharashtra University, Jalgaon, MS 425001 India
| | - Ambalal B. Chaudhari
- School of Life Sciences, Kavayitri Bahinabai Chaudhari North Maharashtra University, Jalgaon, MS 425001 India
| | - Navin D. Dandi
- School of Life Sciences, Kavayitri Bahinabai Chaudhari North Maharashtra University, Jalgaon, MS 425001 India
| |
Collapse
|
43
|
Jawad B, Adhikari P, Cheng K, Podgornik R, Ching WY. Computational Design of Miniproteins as SARS-CoV-2 Therapeutic Inhibitors. Int J Mol Sci 2022; 23:838. [PMID: 35055023 PMCID: PMC8776159 DOI: 10.3390/ijms23020838] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/11/2022] [Accepted: 01/11/2022] [Indexed: 12/20/2022] Open
Abstract
A rational therapeutic strategy is urgently needed for combating SARS-CoV-2 infection. Viral infection initiates when the SARS-CoV-2 receptor-binding domain (RBD) binds to the ACE2 receptor, and thus, inhibiting RBD is a promising therapeutic for blocking viral entry. In this study, the structure of lead antiviral candidate binder (LCB1), which has three alpha-helices (H1, H2, and H3), is used as a template to design and simulate several miniprotein RBD inhibitors. LCB1 undergoes two modifications: structural modification by truncation of the H3 to reduce its size, followed by single and double amino acid substitutions to enhance its binding with RBD. We use molecular dynamics (MD) simulations supported by ab initio density functional theory (DFT) calculations. Complete binding profiles of all miniproteins with RBD have been determined. The MD investigations reveal that the H3 truncation results in a small inhibitor with a -1.5 kcal/mol tighter binding to RBD than original LCB1, while the best miniprotein with higher binding affinity involves D17R or E11V + D17R mutation. DFT calculations provide atomic-scale details on the role of hydrogen bonding and partial charge distribution in stabilizing the minibinder:RBD complex. This study provides insights into general principles for designing potential therapeutics for SARS-CoV-2.
Collapse
Affiliation(s)
- Bahaa Jawad
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO 64110, USA; (B.J.); (P.A.)
- Department of Applied Sciences, University of Technology, Baghdad 10066, Iraq
| | - Puja Adhikari
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO 64110, USA; (B.J.); (P.A.)
| | - Kun Cheng
- Division of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, Kansas City, MO 64108, USA;
| | - Rudolf Podgornik
- Wenzhou Institute of the University of Chinese Academy of Sciences, Wenzhou 325000, China;
- School of Physical Sciences and Kavli Institute of Theoretical Science, University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100090, China
| | - Wai-Yim Ching
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO 64110, USA; (B.J.); (P.A.)
| |
Collapse
|
44
|
Elseginy SA, Anwar MM. Pharmacophore-Based Virtual Screening and Molecular Dynamics Simulation for Identification of a Novel DNA Gyrase B Inhibitor with Benzoxazine Acetamide Scaffold. ACS OMEGA 2022; 7:1150-1164. [PMID: 35036778 PMCID: PMC8756603 DOI: 10.1021/acsomega.1c05732] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 12/14/2021] [Indexed: 05/10/2023]
Abstract
DNA gyrase B is one of the enzyme targets for antimicrobial drug development, and its absence in mammals makes it a suitable target for the creation of safe antibacterial drugs. We identified six novel hits as DNA gyrase B inhibitors in the present study by employing 3D-pharmacophore structure-based virtual screening. The lead compounds complied with drug-likeness rules and lacked toxicity. Compound 4 (ZINC32858011) showed the highest inhibitory activity with an IC50 value of 6.3 ± 0.1 μM against the DNA gyrase enzyme. In contrast, the positive controls ciprofloxacin and novobiocin used in enzyme inhibition assay had IC50 values of 14.4 ± 0.2 and 12.4 ± 0.2 μM, respectively. The molecular docking of the six hits demonstrated that compounds 1, 2, 4, and 6 had suitable fitting modes inside the binding pocket. Molecular dynamics simulations were carried out for the six hits and the rmsd, rmsf, radius of gyration, and solvent accessible surface area parameters obtained from 100 ns molecular dynamics simulations for the six compounds complexed with a DNA gyrase B protein indicated that compound 4 (ZINC32858011) formed the most stable complex with DNA gyrase B. The binding free energy calculation with the MM-PBSA method suggested that the van der Waals interaction, followed by electrostatic force, played a significant role in the binding. Per-residue free binding energy decomposition showed that Ile78 contributed the most for the binding energy followed by Asn46, Asp49, Glu50, Asp73, Ile78, Pro79, Ala86, Ile90, Val120, Thr165, and Val167.
Collapse
Affiliation(s)
- Samia A. Elseginy
- Green
Chemistry Department, Chemical Industries Research Division, National Research Centre, Dokki, Cairo 12622, Egypt
- . Phone: +20(1150882009)
| | - Manal M. Anwar
- Therapeutical
Chemistry Department, National Research
Centre, Dokki, Cairo 12622, Egypt
| |
Collapse
|
45
|
Can docking scoring functions guarantee success in virtual screening? VIRTUAL SCREENING AND DRUG DOCKING 2022. [DOI: 10.1016/bs.armc.2022.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
46
|
Rubio-Martínez J, Jiménez-Alesanco A, Ceballos-Laita L, Ortega-Alarcón D, Vega S, Calvo C, Benítez C, Abian O, Velázquez-Campoy A, Thomson TM, Granadino-Roldán JM, Gómez-Gutiérrez P, Pérez JJ. Discovery of Diverse Natural Products as Inhibitors of SARS-CoV-2 M pro Protease through Virtual Screening. J Chem Inf Model 2021; 61:6094-6106. [PMID: 34806382 PMCID: PMC9931176 DOI: 10.1021/acs.jcim.1c00951] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
SARS-CoV-2 is a type of coronavirus responsible for the international outbreak of respiratory illness termed COVID-19 that forced the World Health Organization to declare a pandemic infectious disease situation of international concern at the beginning of 2020. The need for a swift response against COVID-19 prompted to consider different sources to identify bioactive compounds that can be used as therapeutic agents, including available drugs and natural products. Accordingly, this work reports the results of a virtual screening process aimed at identifying antiviral natural product inhibitors of the SARS-CoV-2 Mpro viral protease. For this purpose, ca. 2000 compounds of the Selleck database of Natural Compounds were the subject of an ensemble docking process targeting the Mpro protease. Molecules that showed binding to most of the protein conformations were retained for a further step that involved the computation of the binding free energy of the ligand-Mpro complex along a molecular dynamics trajectory. The compounds that showed a smooth binding free energy behavior were selected for in vitro testing. From the resulting set of compounds, five compounds exhibited an antiviral profile, and they are disclosed in the present work.
Collapse
Affiliation(s)
- Jaime Rubio-Martínez
- Department
of Materials Science and Physical Chemistry, University of Barcelona and the Institut de Recerca en Quimica Teorica
i Computacional (IQTCUB), 08028 Barcelona, Spain,. Phone: (+34) 93
4039263. Fax: (+34) 93 4021231
| | - Ana Jiménez-Alesanco
- Institute
for Biocomputation and Physics of Complex Systems (BIFI), Joint Units
IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad
de Zaragoza, 50018 Zaragoza, Spain,Departamento
de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50018 Zaragoza, Spain
| | - Laura Ceballos-Laita
- Institute
for Biocomputation and Physics of Complex Systems (BIFI), Joint Units
IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad
de Zaragoza, 50018 Zaragoza, Spain,Instituto
de Investigación Sanitaria de Aragón (IIS Aragon), 50009 Zaragoza, Spain
| | - David Ortega-Alarcón
- Institute
for Biocomputation and Physics of Complex Systems (BIFI), Joint Units
IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad
de Zaragoza, 50018 Zaragoza, Spain,Departamento
de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50018 Zaragoza, Spain
| | - Sonia Vega
- Institute
for Biocomputation and Physics of Complex Systems (BIFI), Joint Units
IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad
de Zaragoza, 50018 Zaragoza, Spain
| | - Cristina Calvo
- Centro
de Investigación Biomédica en Red en el Área
Temática de Enfermedades Hepáticas Digestivas (CIBERehd), 28029 Madrid, Spain,Institute
of Molecular Biology of Barcelona (IBMB-CSIC), 08028 Barcelona, Spain
| | - Cristina Benítez
- Centro
de Investigación Biomédica en Red en el Área
Temática de Enfermedades Hepáticas Digestivas (CIBERehd), 28029 Madrid, Spain,Institute
of Molecular Biology of Barcelona (IBMB-CSIC), 08028 Barcelona, Spain
| | - Olga Abian
- Institute
for Biocomputation and Physics of Complex Systems (BIFI), Joint Units
IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad
de Zaragoza, 50018 Zaragoza, Spain,Departamento
de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50018 Zaragoza, Spain,Instituto
de Investigación Sanitaria de Aragón (IIS Aragon), 50009 Zaragoza, Spain,Centro
de Investigación Biomédica en Red en el Área
Temática de Enfermedades Hepáticas Digestivas (CIBERehd), 28029 Madrid, Spain,Instituto
Aragonés de Ciencias de la Salud (IACS), 50018 Zaragoza, Spain
| | - Adrián Velázquez-Campoy
- Institute
for Biocomputation and Physics of Complex Systems (BIFI), Joint Units
IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad
de Zaragoza, 50018 Zaragoza, Spain,Departamento
de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50018 Zaragoza, Spain,Instituto
de Investigación Sanitaria de Aragón (IIS Aragon), 50009 Zaragoza, Spain,Centro
de Investigación Biomédica en Red en el Área
Temática de Enfermedades Hepáticas Digestivas (CIBERehd), 28029 Madrid, Spain,Fundación
ARAID, Gobierno de Aragón, 50018 Zaragoza, Spain
| | - Timothy M. Thomson
- Centro
de Investigación Biomédica en Red en el Área
Temática de Enfermedades Hepáticas Digestivas (CIBERehd), 28029 Madrid, Spain,Institute
of Molecular Biology of Barcelona (IBMB-CSIC), 08028 Barcelona, Spain,Universidad
Peruana Cayetano Heredia, San Martín
de Porres 15102, Perú
| | - José Manuel Granadino-Roldán
- Departamento
de Química Física y Analítica, Facultad de Ciencias
Experimentales, Universidad de Jaén, Campus “Las Lagunillas”
s/n, 23071, Jaén, Spain
| | - Patricia Gómez-Gutiérrez
- Department
of Chemical Engineering, Universitat Politecnica
de Catalunya- Barcelona Tech, Av. Diagonal, 647, 08028 Barcelona, Spain
| | - Juan J. Pérez
- Department
of Chemical Engineering, Universitat Politecnica
de Catalunya- Barcelona Tech, Av. Diagonal, 647, 08028 Barcelona, Spain
| |
Collapse
|
47
|
Mohd Siddique MU, Thakur A, Shilkar D, Yasmin S, Halakova D, Kovacikova L, Prnova MS, Stefek M, Acevedo O, Dasararaju G, Devadasan V, Mondal SK, Jayaprakash V. Non-carboxylic acid inhibitors of aldose reductase based on N-substituted thiazolidinedione derivatives. Eur J Med Chem 2021; 223:113630. [PMID: 34175538 DOI: 10.1016/j.ejmech.2021.113630] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 06/06/2021] [Accepted: 06/07/2021] [Indexed: 11/22/2022]
Abstract
In search of dually active PPAR-modulators/aldose reductase (ALR2) inhibitors, 16 benzylidene thiazolidinedione derivatives, previously reported as partial PPARγ agonists, together with additional 18 structural congeners, were studied for aldose reductase inhibitory activity. While no compounds had dual property, our efforts led to the identification of promising inhibitors of ALR2. Eight compounds (11, 15-16, 20-24, 30) from the library of 33 compounds were identified as potent and selective inhibitors of ALR2. Compound 21 was the most effective and selective inhibitor with an IC50 value of 0.95 ± 0.11 and 13.52 ± 0.81 μM against ALR2 and aldehyde reductase (ALR1) enzymes, respectively. Molecular docking and dynamics studies were performed to understand inhibitor-enzyme interactions at the molecular level that determine the potency and selectivity. Compound 21 was further subjected to in silico and in vitro studies to evaluate the pharmacokinetic profile. Being less acidic (pKa = 9.8), the compound might have a superior plasma membrane permeability and reach the cytosolic ALR2. This fact together with excellent drug-likeness criteria points to improved bioavailability compared to the clinically used compound Epalrestat. The designed compounds represent a novel group of non-carboxylate inhibitors of aldose reductase with an improved physicochemical profile.
Collapse
Affiliation(s)
- Mohd Usman Mohd Siddique
- Department of Pharmaceutical Sciences & Technology, Mesra, Ranchi, 835215, (JH), India; Department of Pharmaceutical Chemistry, Shri Vile Parle Kelavani Mandal's Institute of Pharmacy, Dhule, 424001, (MH), India.
| | - Abhishek Thakur
- Department of Chemistry, University of Miami, Coral Gables, Florida, 33146, USA.
| | - Deepak Shilkar
- Department of Pharmaceutical Sciences & Technology, Mesra, Ranchi, 835215, (JH), India.
| | - Sabina Yasmin
- Department of Pharmaceutical Sciences & Technology, Mesra, Ranchi, 835215, (JH), India; Department of Pharmaceutical Chemistry, College of Pharmacy, King Khalid University, Abha, 61441, Saudi Arabia.
| | - Dominika Halakova
- Institute of Experimental Pharmacology and Toxicology, CEM, Slovak Academy of Sciences, Bratislava, Slovak Republic.
| | - Lucia Kovacikova
- Institute of Experimental Pharmacology and Toxicology, CEM, Slovak Academy of Sciences, Bratislava, Slovak Republic.
| | - Marta Soltesova Prnova
- Institute of Experimental Pharmacology and Toxicology, CEM, Slovak Academy of Sciences, Bratislava, Slovak Republic.
| | - Milan Stefek
- Institute of Experimental Pharmacology and Toxicology, CEM, Slovak Academy of Sciences, Bratislava, Slovak Republic.
| | - Orlando Acevedo
- Department of Chemistry, University of Miami, Coral Gables, Florida, 33146, USA.
| | - Gayathri Dasararaju
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai, 600025, (TN), India.
| | - Velmurugan Devadasan
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai, 600025, (TN), India.
| | - Susanta Kumar Mondal
- TCG Life Sciences Ltd, Block-EP & GP, BIPL, Tower-B, Saltlake, Sector-V, Kolkata, 700091, (WB), India.
| | | |
Collapse
|
48
|
The role of zinc finger linkers in zinc finger protein binding to DNA. J Comput Aided Mol Des 2021; 35:973-986. [PMID: 34350488 DOI: 10.1007/s10822-021-00413-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 07/26/2021] [Indexed: 10/20/2022]
Abstract
Zinc finger proteins (ZFP) play important roles in cellular processes. The DNA binding region of ZFP consists of 3 zinc finger DNA binding domains connected by amino acid linkers, the sequence TGQKP connects ZF1 and ZF2, and TGEKP connects ZF2 with ZF3. Linkers act to tune the zinc finger protein in the right position to bind its DNA target, the type of amino acid residues and length of linkers reflect on ZF1-ZF2-ZF3 interactions and contribute to the search and recognition process of ZF protein to its DNA target. Linker mutations and the affinity of the resulting mutants to specific and nonspecific DNA targets were studied by MD simulations and MM_GB(PB)SA. The affinity of mutants to DNA varied with type and position of amino acid residue. Mutation of K in TGQKP resulted in loss in affinity due to the loss of positive K interaction with phosphates, mutation of G showed loss in affinity to DNA, WT protein and all linker mutants showed loss in affinity to a nonspecific DNA target, this finding confirms previous reports which interpreted this loss in affinity as due to ZF1 having an anchoring role, and ZF3 playing an explorer role in the binding mechanism. The change in ZFP-DNA affinity with linker mutations is discussed in view of protein structure and role of linker residues in binding.
Collapse
|
49
|
Search for Novel Lead Inhibitors of Yeast Cytochrome bc1, from Drugbank and COCONUT. Molecules 2021; 26:molecules26144323. [PMID: 34299598 PMCID: PMC8307329 DOI: 10.3390/molecules26144323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/12/2021] [Accepted: 07/14/2021] [Indexed: 11/17/2022] Open
Abstract
In this work we introduce a novel filtering and molecular modeling pipeline based on a fingerprint and descriptor similarity procedure, coupled with molecular docking and molecular dynamics (MD), to select potential novel quoinone outside inhibitors (QoI) of cytochrome bc1 with the aim of determining the same or different chromophores to usual. The study was carried out using the yeast cytochrome bc1 complex with its docked ligand (stigmatellin), using all the fungicides from FRAC code C3 mode of action, 8617 Drugbank compounds and 401,624 COCONUT compounds. The introduced drug repurposing pipeline consists of compound similarity with C3 fungicides and molecular docking (MD) simulations with final QM/MM binding energy determination, while aiming for potential novel chromophores and perserving at least an amide (R1HN(C=O)R2) or ester functional group of almost all up to date C3 fungicides. 3D descriptors used for a similarity test were based on the 280 most stable Padel descriptors. Hit compounds that passed fingerprint and 3D descriptor similarity condition and had either an amide or an ester group were submitted to docking where they further had to satisfy both Chemscore fitness and specific conformation constraints. This rigorous selection resulted in a very limited number of candidates that were forwarded to MD simulations and QM/MM binding affinity estimations by the ORCA DFT program. In this final step, stringent criteria based on (a) sufficiently high frequency of H-bonds; (b) high interaction energy between protein and ligand through the whole MD trajectory; and (c) high enough QM/MM binding energy scores were applied to further filter candidate inhibitors. This elaborate search pipeline led finaly to four Drugbank synthetic lead compounds (DrugBank) and seven natural (COCONUT database) lead compounds—tentative new inhibitors of cytochrome bc1. These eleven lead compounds were additionally validated through a comparison of MM/PBSA free binding energy for new leads against those obtatined for 19 QoIs.
Collapse
|
50
|
Santo AAE, Feliciano GT. Genetic Algorithms Applied to Thermodynamic Rational Design of Mimetic Antibodies Based on the GB1 Domain of Streptococcal Protein G: An Atomistic Simulation Study. J Phys Chem B 2021; 125:7985-7996. [PMID: 34264671 DOI: 10.1021/acs.jpcb.1c03324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The development of mimetic antibodies (MA) capable of combining the high affinity and selectivity of antibodies with the small size of the peptides has enormous potential for applications in current biotechnology. In this work, we demonstrate that in silico MA design is possible through genetic algorithms (GA) developed from shell scripts capable of combining software commonly used for atomistic simulation. Our results demonstrate that, using the GB1 domain of the streptococcal G protein as a model, it is possible to optimize the molecular recognition capacity of a large MA population in a few generations. In the first case, GA was able to generate 10 MA with binding free energy (BFE) less than the vascular endothelial cell growth factor conjugated with the fms-type tyrosine kinase receptor. In the second case, it generated 13 MA with BFE less than that of the hepatitis C-E2 viral envelope conjugate with the antibody. Through the GA developed in this work, we demonstrate the use of a new protocol, capable of guiding experimental methods for the design of bioactive peptides that can assist in the development of new therapeutic molecules.
Collapse
Affiliation(s)
- Anderson A E Santo
- Institute of Chemistry, São Paulo State University, Araraquara, SP, Brazil
| | | |
Collapse
|