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Bayıl I, Sarowar Hossain M, Tamanna S, Jamir Uddin M, Mashood Ahamed FM, Jardan YAB, Bourhia M, Taskin Tok T. Aptamer biosensor design for the detection of endocrine-disrupting chemicals small organic molecules using novel bioinformatics methods. J Mol Graph Model 2024; 131:108785. [PMID: 38820705 DOI: 10.1016/j.jmgm.2024.108785] [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: 03/07/2024] [Revised: 04/25/2024] [Accepted: 04/29/2024] [Indexed: 06/02/2024]
Abstract
Endocrine-disrupting chemicals (EDCs) are substances that can disrupt the normal functioning of hormones.Using aptamers, which are biological recognition elements, biosensors can quickly and accurately detect EDCs in environmental samples. However, the elucidation of aptamer structures by conventional methods is highly challenging due to their complexity. This has led to the development of three-dimensional aptamer structures based on different models and techniques. To do this, we developed a way to predict the 3D structures of the SS DNA needed for this sequence by starting with an aptamer sequence that has biosensor properties specific to bisphenol-A (BPA), one of the chemicals found in water samples that can interfere with hormones. In addition, we will elucidate the intermolecular mechanisms and binding affinity between aptamers and endocrine disruptors using bioinformatics techniques such as molecular docking, molecular dynamics simulation, and binding energies. The outcomes of our study are to compare modeling programs and force fields to see how reliable they are and how well they agree with results found in the existing literature, to understand the intermolecular mechanisms and affinity of aptamer-based biosensors, and to find a new way to make aptamers that takes less time and costs less.
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Affiliation(s)
- Imren Bayıl
- Department of Bioinformatics and Computational Biology, Gaziantep University, Turkey.
| | - Md Sarowar Hossain
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Birulia 1216, Ashulia, Dhaka, Bangladesh; Faculty of Pharmaceutical Science, Assam Down Town University, Guwahati, Assam, India.
| | - Sonia Tamanna
- Department of Biochemistry and Molecular Biology, University of Dhaka. Dhaka-1000, Bangladesh.
| | - Md Jamir Uddin
- Department of Chemistry, Hajee Mohammad Danesh Science and Technology University, Dinajpur, 5200, Bangladesh.
| | - F M Mashood Ahamed
- PG and Research Department of Chemistry, Jamal Mohamed College (Autonomous), Tiruchirappalli, 620020, India; Affiliated to Bharathidasan University, Tamilnadu, India.
| | - Yousef A Bin Jardan
- Department of Pharmaceutics, College of Pharmacy, King Saud University, P.O. Box 11451, Riyadh, Saudi Arabia.
| | - Mohammed Bourhia
- Department of Chemistry and Biochemistry, Faculty of Medicine and Pharmacy, Ibn Zohr University, Laayoune 70000, Morocco.
| | - Tugba Taskin Tok
- Faculty of Science, Department of Chemistry, Gaziantep University, Turkey.
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2
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Katzberger P, Riniker S. A general graph neural network based implicit solvation model for organic molecules in water. Chem Sci 2024; 15:10794-10802. [PMID: 39027274 PMCID: PMC11253111 DOI: 10.1039/d4sc02432j] [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: 04/12/2024] [Accepted: 05/24/2024] [Indexed: 07/20/2024] Open
Abstract
The dynamical behavior of small molecules in their environment can be studied with classical molecular dynamics (MD) simulations to gain deeper insight on an atomic level and thus complement and rationalize the interpretation of experimental findings. Such approaches are of great value in various areas of research, e.g., in the development of new therapeutics. The accurate description of solvation effects in such simulations is thereby key and has in consequence been an active field of research since the introduction of MD. So far, the most accurate approaches involve computationally expensive explicit solvent simulations, while widely applied models using an implicit solvent description suffer from reduced accuracy. Recently, machine learning (ML) approaches that provide a probabilistic representation of solvation effects have been proposed as potential alternatives. However, the associated computational costs and minimal or lack of transferability render them unusable in practice. Here, we report the first example of a transferable ML-based implicit solvent model trained on a diverse set of 3 000 000 molecular structures that can be applied to organic small molecules for simulations in water. Extensive testing against reference calculations demonstrated that the model delivers on par accuracy with explicit solvent simulations while providing an up to 18-fold increase in sampling rate.
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Affiliation(s)
- Paul Katzberger
- Department of Chemistry and Applied Biosciences, ETH Zürich Vladimir-Prelog-Weg 2 8093 Zürich Switzerland
| | - Sereina Riniker
- Department of Chemistry and Applied Biosciences, ETH Zürich Vladimir-Prelog-Weg 2 8093 Zürich Switzerland
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3
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Duarte T, Omage FB, Rieder GS, Rocha JBT, Dalla Corte CL. Investigating SARS-CoV-2 virus-host interactions and mRNA expression: Insights using three models of D. melanogaster. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167324. [PMID: 38925484 DOI: 10.1016/j.bbadis.2024.167324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 04/22/2024] [Accepted: 06/19/2024] [Indexed: 06/28/2024]
Abstract
Responsible for COVID-19, SARS-CoV-2 is a coronavirus in which contagious variants continue to appear. Therefore, some population groups have demonstrated greater susceptibility to contagion and disease progression. For these reasons, several researchers have been studying the SARS-CoV-2/human interactome to understand the pathophysiology of COVID-19 and develop new pharmacological strategies. D. melanogaster is a versatile animal model with approximately 90 % human protein orthology related to SARS-CoV-2/human interactome and is widely used in metabolic studies. In this context, our work assessed the potential interaction between human proteins (ZNF10, NUP88, BCL2L1, UBC9, and RBX1) and their orthologous proteins in D. melanogaster (gl, Nup88, Buffy, ubc9, and Rbx1a) with proteins from SARS-CoV-2 (nsp3, nsp9, E, ORF7a, N, and ORF10) using computational approaches. Our results demonstrated that all the proteins have the potential to interact, and we compared the binding sites between humans and fruit flies. The stability and consistency in the structure of the gl_nsp3 complex, specifically, could be crucial for its specific biological functions. Lastly, to enhance the understanding of the influence of host factors on coronavirus infection, we also analyse the mRNA expression of the five genes (mbo, gl, lwr, Buffy, and Roc1a) responsible for encoding the fruit fly proteins. Briefly, we demonstrated that those genes were differentially regulated according to diets, sex, and age. Two groups showed higher positive gene regulation than others: females in the HSD group and males in the aging group, which could imply a higher virus-host susceptibility. Overall, while preliminary, our work contributes to the understanding of host defense mechanisms and potentially identifies candidate proteins and genes for in vivo viral studies against SARS-CoV-2.
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Affiliation(s)
- Tâmie Duarte
- Laboratory of Experimental Biochemistry and Toxicology, Department of Biochemistry and Molecular Biology, Center of Natural and Exact Sciences, Federal University of Santa Maria, 1000 Roraima Avenue, Santa Maria, RS 97105-900, Brazil; Department of Biochemistry and Molecular Biology, Federal University of Santa Maria, 1000 Roraima Avenue, Santa Maria, RS 97105-900, Brazil
| | - Folorunsho Bright Omage
- Biological Chemistry Laboratory, Department of Organic Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, SP, Brazil; Computational Biology Research Group, Embrapa Agricultural Informatics, Campinas, SP, Brazil
| | - Guilherme Schmitt Rieder
- Department of Biochemistry and Molecular Biology, Federal University of Santa Maria, 1000 Roraima Avenue, Santa Maria, RS 97105-900, Brazil
| | - João B T Rocha
- Department of Biochemistry and Molecular Biology, Federal University of Santa Maria, 1000 Roraima Avenue, Santa Maria, RS 97105-900, Brazil
| | - Cristiane Lenz Dalla Corte
- Laboratory of Experimental Biochemistry and Toxicology, Department of Biochemistry and Molecular Biology, Center of Natural and Exact Sciences, Federal University of Santa Maria, 1000 Roraima Avenue, Santa Maria, RS 97105-900, Brazil; Department of Biochemistry and Molecular Biology, Federal University of Santa Maria, 1000 Roraima Avenue, Santa Maria, RS 97105-900, Brazil.
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4
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Ahad Hossain M, Sultana S, Alanazi MM, Hadni H, Bhat AR, Hasan I, Kawsar SM. In vitro antimicrobial, anticancer evaluation, and in silico studies of mannopyranoside analogs against bacterial and fungal proteins: Acylation leads to improved antimicrobial activity. Saudi Pharm J 2024; 32:102093. [PMID: 38737807 PMCID: PMC11087236 DOI: 10.1016/j.jsps.2024.102093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Accepted: 04/28/2024] [Indexed: 05/14/2024] Open
Abstract
Carbohydrate analogs are an important, well-established class of clinically useful medicinal agents that exhibit potent antimicrobial activity. Thus, we explored the various therapeutic potential of methyl α-D-mannopyranoside (MαDM) analogs, including their ability to synthesize and assess their antibacterial, antifungal, and anticancer properties; additionally, molecular docking, molecular dynamics simulation, and ADMET analysis were performed. The structure of the synthesized MαDM analogs was ascertained by spectroscopic techniques and physicochemical and elemental analysis. In vitro antimicrobial activity was assessed and revealed significant inhibitory effects, particularly against gram-negative bacteria along with the prediction of activity spectra for substances (PASS). Concurrently, MαDM analogs showed good results against antifungal pathogens and exhibited promising anticancer effects in vitro, demonstrating dose-dependent cytotoxicity against Ehrlich ascites carcinoma (EAC) cancer cells while sparing normal cells from compound 5, with an IC50 of 4511.65 µg/mL according to the MTT colorimetric assay. A structure-activity relationship (SAR) study revealed that hexose combined with the acyl chains of decanoyl (C-10) and benzenesulfonyl (C6H5SO2-) had synergistic effects on the bacteria and fungi that were examined. Molecular docking was performed against the Escherichia coli (6KZV) and Candida albicans (1EAG) proteins to acquire insights into the molecular interactions underlying the observed biological activities. The docking results were further supported by 100 ns molecular dynamics simulations, which provided a dynamic view of the stability and flexibility of complexes involving MαDM and its targets. In addition, ADMET analysis was used to evaluate the toxicological and pharmacokinetic profiles. Owing to their promising drug-like properties, these MαDM analogs exhibit potential as prospective therapeutic candidates for future development.
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Affiliation(s)
- Md. Ahad Hossain
- Laboratory of Carbohydrate and Nucleoside Chemistry (LCNC), Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong 4331, Bangladesh
| | - Shahin Sultana
- Laboratory of Carbohydrate and Nucleoside Chemistry (LCNC), Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong 4331, Bangladesh
| | - Mohammed M. Alanazi
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Hanine Hadni
- LIMAS, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Ajmal R. Bhat
- Department of Chemistry, RTM Nagpur University, Nagpur 440033, India
| | - Imtiaj Hasan
- Department of Biochemistry and Molecular Biology, Faculty of Science, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Sarkar M.A. Kawsar
- Laboratory of Carbohydrate and Nucleoside Chemistry (LCNC), Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong 4331, Bangladesh
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5
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Gonzalez-Llerena JL, Espinosa-Rodriguez BA, Treviño-Almaguer D, Mendez-Lopez LF, Carranza-Rosales P, Gonzalez-Barranco P, Guzman-Delgado NE, Romo-Mancillas A, Balderas-Renteria I. Cordycepin Triphosphate as a Potential Modulator of Cellular Plasticity in Cancer via cAMP-Dependent Pathways: An In Silico Approach. Int J Mol Sci 2024; 25:5692. [PMID: 38891880 PMCID: PMC11171877 DOI: 10.3390/ijms25115692] [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: 04/05/2024] [Revised: 05/14/2024] [Accepted: 05/21/2024] [Indexed: 06/21/2024] Open
Abstract
Cordycepin, or 3'-deoxyadenosine, is an adenosine analog with a broad spectrum of biological activity. The key structural difference between cordycepin and adenosine lies in the absence of a hydroxyl group at the 3' position of the ribose ring. Upon administration, cordycepin can undergo an enzymatic transformation in specific tissues, forming cordycepin triphosphate. In this study, we conducted a comprehensive analysis of the structural features of cordycepin and its derivatives, contrasting them with endogenous purine-based metabolites using chemoinformatics and bioinformatics tools in addition to molecular dynamics simulations. We tested the hypothesis that cordycepin triphosphate could bind to the active site of the adenylate cyclase enzyme. The outcomes of our molecular dynamics simulations revealed scores that are comparable to, and superior to, those of adenosine triphosphate (ATP), the endogenous ligand. This interaction could reduce the production of cyclic adenosine monophosphate (cAMP) by acting as a pseudo-ATP that lacks a hydroxyl group at the 3' position, essential to carry out nucleotide cyclization. We discuss the implications in the context of the plasticity of cancer and other cells within the tumor microenvironment, such as cancer-associated fibroblast, endothelial, and immune cells. This interaction could awaken antitumor immunity by preventing phenotypic changes in the immune cells driven by sustained cAMP signaling. The last could be an unreported molecular mechanism that helps to explain more details about cordycepin's mechanism of action.
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Affiliation(s)
- Jose Luis Gonzalez-Llerena
- Laboratory of Molecular Pharmacology and Biological Models, School of Chemistry, Autonomous University of Nuevo Leon, San Nicolas de los Garza 66451, Mexico; (J.L.G.-L.); (B.A.E.-R.); (D.T.-A.); (P.G.-B.)
- Center for Research on Nutrition and Public Health, School of Public Health and Nutrition, Autonomous University of Nuevo Leon, Monterrey 66460, Mexico;
| | - Bryan Alejandro Espinosa-Rodriguez
- Laboratory of Molecular Pharmacology and Biological Models, School of Chemistry, Autonomous University of Nuevo Leon, San Nicolas de los Garza 66451, Mexico; (J.L.G.-L.); (B.A.E.-R.); (D.T.-A.); (P.G.-B.)
| | - Daniela Treviño-Almaguer
- Laboratory of Molecular Pharmacology and Biological Models, School of Chemistry, Autonomous University of Nuevo Leon, San Nicolas de los Garza 66451, Mexico; (J.L.G.-L.); (B.A.E.-R.); (D.T.-A.); (P.G.-B.)
| | - Luis Fernando Mendez-Lopez
- Center for Research on Nutrition and Public Health, School of Public Health and Nutrition, Autonomous University of Nuevo Leon, Monterrey 66460, Mexico;
| | - Pilar Carranza-Rosales
- Laboratory of Cell Biology, Northeast Biomedical Research Center, Mexican Social Security Institute, Monterrey 64720, Mexico;
| | - Patricia Gonzalez-Barranco
- Laboratory of Molecular Pharmacology and Biological Models, School of Chemistry, Autonomous University of Nuevo Leon, San Nicolas de los Garza 66451, Mexico; (J.L.G.-L.); (B.A.E.-R.); (D.T.-A.); (P.G.-B.)
| | - Nancy Elena Guzman-Delgado
- Health Research Division, High Specialty Medical Unit, Cardiology Hospital N. 34. Mexican Social Security Institute, Monterrey 64360, Mexico;
| | - Antonio Romo-Mancillas
- Computer Aided Drug Design and Synthesis Group, School of Chemistry, Autonomous University of Queretaro, Queretaro 76010, Mexico
| | - Isaias Balderas-Renteria
- Laboratory of Molecular Pharmacology and Biological Models, School of Chemistry, Autonomous University of Nuevo Leon, San Nicolas de los Garza 66451, Mexico; (J.L.G.-L.); (B.A.E.-R.); (D.T.-A.); (P.G.-B.)
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6
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de Souza BB, Meegoda J. Insights into PFAS environmental fate through computational chemistry: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:171738. [PMID: 38494023 DOI: 10.1016/j.scitotenv.2024.171738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 02/28/2024] [Accepted: 03/14/2024] [Indexed: 03/19/2024]
Abstract
Per- and polyfluoroalkyl substances (PFAS) are widely used chemicals that exhibit exceptional chemical and thermal stability. However, their resistance to degradation has led to their widespread environmental contamination. PFAS also negatively affect the environment and other organisms, highlighting the need for effective remediation methods to mitigate their presence and prevent further contamination. Computational chemistry methods, such as Density Functional Theory (DFT) and Molecular Dynamics (MD) offer valuable tools for studying PFAS and simulating their interactions with other molecules. This review explores how computational chemistry methods contribute to understanding and tackling PFAS in the environment. PFAS have been extensively studied using DFT and MD, each method offering unique advantages and computational limitations. MD simulates large macromolecules systems however it lacks the ability model chemical reactions, while DFT provides molecular insights however at a high computational cost. The integration of DFT with MD shows promise in predicting PFAS behavior in different environments. This work summarizes reported studies on PFAS compounds, focusing on adsorption, destruction, and bioaccumulation, highlighting contributions of computational methods while discussing the need for continued research. The findings emphasize the importance of computational chemistry in addressing PFAS contamination, guiding risk assessments, and informing future research and innovations in this field.
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Affiliation(s)
- Bruno Bezerra de Souza
- John A. Reif, Jr. Department of Civil and Environmental Engineering, New Jersey Institute of Technology, Newark, NJ 07102, USA
| | - Jay Meegoda
- John A. Reif, Jr. Department of Civil and Environmental Engineering, New Jersey Institute of Technology, Newark, NJ 07102, USA.
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7
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Chen S, Yan K, Liu B. PDB-BRE: A ligand-protein interaction binding residue extractor based on Protein Data Bank. Proteins 2024; 92:145-153. [PMID: 37750380 DOI: 10.1002/prot.26596] [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: 05/20/2023] [Revised: 08/13/2023] [Accepted: 09/11/2023] [Indexed: 09/27/2023]
Abstract
Proteins typically exert their biological functions by interacting with other biomolecules or ligands. The study of ligand-protein interactions is crucial in elucidating the biological mechanisms of proteins. Most existing studies have focused on analyzing ligand-protein interactions, and they ignore the additional situational of inserted and modified residues. Besides, the resources often support only a single ligand type and cannot obtain satisfied results in analyzing novel complexes. Therefore, it is important to develop a general analytical tool to extract the binding residues of ligand-protein interactions in complexes fully. In this study, we propose a ligand-protein interaction binding residue extractor (PDB-BRE), which can be used to automatically extract interacting ligand or protein-binding residues from complex three-dimensional (3D) structures based on the RCSB Protein Data Bank (RCSB PDB). PDB-BRE offers a notable advantage in its comprehensive support for analyzing six distinct types of ligands, including proteins, peptides, DNA, RNA, mixed DNA and RNA entities, and non-polymeric entities. Moreover, it takes into account the consideration of inserted and modified residues within complexes. Compared to other state-of-the-art methods, PDB-BRE is more suitable for massively parallel batch analysis, and can be directly applied for downstream tasks, such as predicting binding residues of novel complexes. PDB-BRE is freely available at http://bliulab.net/PDB-BRE.
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Affiliation(s)
- Shutao Chen
- School of Computer Science and Technology, Beijing Institute of Technology, Beijing, China
| | - Ke Yan
- School of Computer Science and Technology, Beijing Institute of Technology, Beijing, China
| | - Bin Liu
- School of Computer Science and Technology, Beijing Institute of Technology, Beijing, China
- Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing, China
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8
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Menchon G, Maveyraud L, Czaplicki G. Molecular Dynamics as a Tool for Virtual Ligand Screening. Methods Mol Biol 2024; 2714:33-83. [PMID: 37676592 DOI: 10.1007/978-1-0716-3441-7_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
Rational drug design is essential for new drugs to emerge, especially when the structure of a target protein or nucleic acid is known. To that purpose, high-throughput virtual ligand screening campaigns aim at discovering computationally new binding molecules or fragments to modulate particular biomolecular interactions or biological activities, related to a disease process. The structure-based virtual ligand screening process primarily relies on docking methods which allow predicting the binding of a molecule to a biological target structure with a correct conformation and the best possible affinity. The docking method itself is not sufficient as it suffers from several and crucial limitations (lack of full protein flexibility information, no solvation and ion effects, poor scoring functions, and unreliable molecular affinity estimation).At the interface of computer techniques and drug discovery, molecular dynamics (MD) allows introducing protein flexibility before or after a docking protocol, refining the structure of protein-drug complexes in the presence of water, ions, and even in membrane-like environments, describing more precisely the temporal evolution of the biological complex and ranking these complexes with more accurate binding energy calculations. In this chapter, we describe the up-to-date MD, which plays the role of supporting tools in the virtual ligand screening (VS) process.Without a doubt, using docking in combination with MD is an attractive approach in structure-based drug discovery protocols nowadays. It has proved its efficiency through many examples in the literature and is a powerful method to significantly reduce the amount of required wet experimentations (Tarcsay et al, J Chem Inf Model 53:2990-2999, 2013; Barakat et al, PLoS One 7:e51329, 2012; De Vivo et al, J Med Chem 59:4035-4061, 2016; Durrant, McCammon, BMC Biol 9:71-79, 2011; Galeazzi, Curr Comput Aided Drug Des 5:225-240, 2009; Hospital et al, Adv Appl Bioinforma Chem 8:37-47, 2015; Jiang et al, Molecules 20:12769-12786, 2015; Kundu et al, J Mol Graph Model 61:160-174, 2015; Mirza et al, J Mol Graph Model 66:99-107, 2016; Moroy et al, Future Med Chem 7:2317-2331, 2015; Naresh et al, J Mol Graph Model 61:272-280, 2015; Nichols et al, J Chem Inf Model 51:1439-1446, 2011; Nichols et al, Methods Mol Biol 819:93-103, 2012; Okimoto et al, PLoS Comput Biol 5:e1000528, 2009; Rodriguez-Bussey et al, Biopolymers 105:35-42, 2016; Sliwoski et al, Pharmacol Rev 66:334-395, 2014).
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Affiliation(s)
- Grégory Menchon
- Inserm U1242, Oncogenesis, Stress and Signaling (OSS), Université de Rennes 1, Rennes, France
| | - Laurent Maveyraud
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - Georges Czaplicki
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France.
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9
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Guidetti L, Zappia A, Scalvini L, Ferrari FR, Giorgio C, Castelli R, Galvani F, Vacondio F, Rivara S, Mor M, Urbinati C, Rusnati M, Tognolini M, Lodola A. Molecular Determinants of EphA2 and EphB2 Antagonism Enable the Design of Ligands with Improved Selectivity. J Chem Inf Model 2023; 63:6900-6911. [PMID: 37910792 PMCID: PMC10647059 DOI: 10.1021/acs.jcim.3c01064] [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: 07/13/2023] [Revised: 10/13/2023] [Accepted: 10/18/2023] [Indexed: 11/03/2023]
Abstract
With the aim of identifying novel antagonists selective for the EphA receptor family, a combined experimental and computational approach was taken to investigate the molecular basis of the recognition between a prototypical Eph-ephrin antagonist (UniPR1447) and two representative receptors of the EphA and EphB subfamilies, namely, EphA2 and EphB2 receptors. The conformational free-energy surface (FES) of the binding state of UniPR1447 within the ligand binding domain of EphA2 and EphB2, reconstructed from molecular dynamics (MD) simulations performed on the microsecond time scale, was exploited to drive the design and synthesis of a novel antagonist selective for EphA2 over the EphB2 receptor. The availability of compounds with this pharmacological profile will help discriminate the importance of these two receptors in the insurgence and progression of cancer.
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Affiliation(s)
- Lorenzo Guidetti
- Dipartimento
di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, I- 43124 Parma, Italy
| | - Alfonso Zappia
- Dipartimento
di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, I- 43124 Parma, Italy
| | - Laura Scalvini
- Dipartimento
di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, I- 43124 Parma, Italy
| | - Francesca Romana Ferrari
- Dipartimento
di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, I- 43124 Parma, Italy
| | - Carmine Giorgio
- Dipartimento
di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, I- 43124 Parma, Italy
| | - Riccardo Castelli
- Dipartimento
di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, I- 43124 Parma, Italy
| | - Francesca Galvani
- Dipartimento
di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, I- 43124 Parma, Italy
| | - Federica Vacondio
- Dipartimento
di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, I- 43124 Parma, Italy
| | - Silvia Rivara
- Dipartimento
di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, I- 43124 Parma, Italy
| | - Marco Mor
- Dipartimento
di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, I- 43124 Parma, Italy
- Microbiome
Research Hub, Università degli Studi
di Parma, Parco Area
delle scienze 11/A, I- 43124 Parma, Italy
| | - Chiara Urbinati
- Dipartimento
di Medicina Molecolare Traslazionale, Università
degli Studi di Brescia, Brescia 25121, Italy
| | - Marco Rusnati
- Dipartimento
di Medicina Molecolare Traslazionale, Università
degli Studi di Brescia, Brescia 25121, Italy
| | - Massimiliano Tognolini
- Dipartimento
di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, I- 43124 Parma, Italy
| | - Alessio Lodola
- Dipartimento
di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, I- 43124 Parma, Italy
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10
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Manikandan A, Jeevitha S, Vusa L. Peptidomimetics for CVD screened via TRADD-TRAF2 complex interface assessments. In Silico Pharmacol 2023; 11:28. [PMID: 37899969 PMCID: PMC10611682 DOI: 10.1007/s40203-023-00166-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 10/04/2023] [Indexed: 10/31/2023] Open
Abstract
The main aim of this study is to screen and develop Peptidomimetics to treat atherosclerosis (AS) which is a Cardio Vascular Disease (CVD). Peptidomimetics were obtained from the protein-protein interaction interface of TRADD (Tumor necrosis factor receptor type 1-associated DEATH domain protein) and TRAF2 (TNF receptor-associated factor 2) complex. TRADD-TRAF2 interaction is critical in AS pathogenesis since it assists a series of signal transducers that activate NF-κB. Conceptually, the triggered NF-κB makes an extensive amount of nitric oxide (NO) synthesized by inducible nitric oxide synthase (iNOS), which boons the progress of AS. The examined TRADD-TRAF2 complex (PDB ID: 1F3V) and its interaction details revealed that the sequence range W11-G165 of TRADD highly interacts with TRAF2. The sequence range W11-G165 was selected for the design and preparation of the inhibitory peptide in silico. The selected sequence was mutated with the alanine scanning method to have a range of inhibitory peptides. With the help of different in silico tools, the top three, namely MIP11-25 L, MIP131-143 h, and MIP149-164 m peptides showed the best interaction with the critical residues of TRAF2. Thus, these three peptides were used for generating peptidomimetics using pepMMsMIMIC, a peptidomimetics virtual screening tool. Around 600 peptidomimetics were identified & and retrieved for further screening by employing molecular docking tools and MD (Molecular Dynamics) simulations. Density Functional Theory (DFT) and ADMET predictions were applied to validate the screened peptidomimetics druggability. In the results, peptidomimic compounds MMs03918858 and MMs03927281 with binding energy values of -9.6 kcal/mol and - 9.1 kcal/mol respectively were screened as the best and are proposed for further pre-clinical studies.
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Affiliation(s)
- A Manikandan
- Dept. of Microbiology, M.S. Ramaiah College of Arts, Science and Commerce, Bengaluru, 560054 India
| | - S Jeevitha
- Dept. of Biochemistry, M.S. Ramaiah College of Arts, Science and Commerce, Bengaluru, 560054 India
| | - Laharika Vusa
- Dept. of Microbiology, M.S. Ramaiah College of Arts, Science and Commerce, Bengaluru, 560054 India
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11
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Deeks HM, Zinovjev K, Barnoud J, Mulholland AJ, van der Kamp MW, Glowacki DR. Free energy along drug-protein binding pathways interactively sampled in virtual reality. Sci Rep 2023; 13:16665. [PMID: 37794083 PMCID: PMC10551034 DOI: 10.1038/s41598-023-43523-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/25/2023] [Indexed: 10/06/2023] Open
Abstract
We describe a two-step approach for combining interactive molecular dynamics in virtual reality (iMD-VR) with free energy (FE) calculation to explore the dynamics of biological processes at the molecular level. We refer to this combined approach as iMD-VR-FE. Stage one involves using a state-of-the-art 'human-in-the-loop' iMD-VR framework to generate a diverse range of protein-ligand unbinding pathways, benefitting from the sophistication of human spatial and chemical intuition. Stage two involves using the iMD-VR-sampled pathways as initial guesses for defining a path-based reaction coordinate from which we can obtain a corresponding free energy profile using FE methods. To investigate the performance of the method, we apply iMD-VR-FE to investigate the unbinding of a benzamidine ligand from a trypsin protein. The binding free energy calculated using iMD-VR-FE is similar for each pathway, indicating internal consistency. Moreover, the resulting free energy profiles can distinguish energetic differences between pathways corresponding to various protein-ligand conformations (e.g., helping to identify pathways that are more favourable) and enable identification of metastable states along the pathways. The two-step iMD-VR-FE approach offers an intuitive way for researchers to test hypotheses for candidate pathways in biomolecular systems, quickly obtaining both qualitative and quantitative insight.
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Affiliation(s)
- Helen M Deeks
- Center for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
| | - Kirill Zinovjev
- Departamento de Química Física, Universidad de Valencia, 46100, Burjassot, Spain
- School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK
| | - Jonathan Barnoud
- Center for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
- CiTIUS | Centro Singular de Investigación en Tecnoloxías Intelixentes da USC, Rúa de Jenaro de la Fuente, s/n, 15705, Santiago de Compostela, A Coruña, Spain
| | - Adrian J Mulholland
- Center for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
| | - Marc W van der Kamp
- Center for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK.
- School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK.
| | - David R Glowacki
- CiTIUS | Centro Singular de Investigación en Tecnoloxías Intelixentes da USC, Rúa de Jenaro de la Fuente, s/n, 15705, Santiago de Compostela, A Coruña, Spain.
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12
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Pratap Reddy Gajulapalli V. Development of Kinase-Centric Drugs: A Computational Perspective. ChemMedChem 2023; 18:e202200693. [PMID: 37442809 DOI: 10.1002/cmdc.202200693] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 07/12/2023] [Accepted: 07/12/2023] [Indexed: 07/15/2023]
Abstract
Kinases are prominent drug targets in the pharmaceutical and research community due to their involvement in signal transduction, physiological responses, and upon dysregulation, in diseases such as cancer, neurological and autoimmune disorders. Several FDA-approved small-molecule drugs have been developed to combat human diseases since Gleevec was approved for the treatment of chronic myelogenous leukemia. Kinases were considered "undruggable" in the beginning. Several FDA-approved small-molecule drugs have become available in recent years. Most of these drugs target ATP-binding sites, but a few target allosteric sites. Among kinases that belong to the same family, the catalytic domain shows high structural and sequence conservation. Inhibitors of ATP-binding sites can cause off-target binding. Because members of the same family have similar sequences and structural patterns, often complex relationships between kinases and inhibitors are observed. To design and develop drugs with desired selectivity, it is essential to understand the target selectivity for kinase inhibitors. To create new inhibitors with the desired selectivity, several experimental methods have been designed to profile the kinase selectivity of small molecules. Experimental approaches are often expensive, laborious, time-consuming, and limited by the available kinases. Researchers have used computational methodologies to address these limitations in the design and development of effective therapeutics. Many computational methods have been developed over the last few decades, either to complement experimental findings or to forecast kinase inhibitor activity and selectivity. The purpose of this review is to provide insight into recent advances in theoretical/computational approaches for the design of new kinase inhibitors with the desired selectivity and optimization of existing inhibitors.
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13
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Akash S, Bayıl I, Hossain MS, Islam MR, Hosen ME, Mekonnen AB, Nafidi HA, Bin Jardan YA, Bourhia M, Bin Emran T. Novel computational and drug design strategies for inhibition of human papillomavirus-associated cervical cancer and DNA polymerase theta receptor by Apigenin derivatives. Sci Rep 2023; 13:16565. [PMID: 37783745 PMCID: PMC10545697 DOI: 10.1038/s41598-023-43175-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 09/20/2023] [Indexed: 10/04/2023] Open
Abstract
The present study deals with the advanced in-silico analyses of several Apigenin derivatives to explore human papillomavirus-associated cervical cancer and DNA polymerase theta inhibitor properties by molecular docking, molecular dynamics, QSAR, drug-likeness, PCA, a dynamic cross-correlation matrix and quantum calculation properties. The initial literature study revealed the potent antimicrobial and anticancer properties of Apigenin, prompting the selection of its potential derivatives to investigate their abilities as inhibitors of human papillomavirus-associated cervical cancer and DNA polymerase theta. In silico molecular docking was employed to streamline the findings, revealing promising energy-binding interactions between all Apigenin derivatives and the targeted proteins. Notably, Apigenin 4'-O-Rhamnoside and Apigenin-4'-Alpha-L-Rhamnoside demonstrated higher potency against the HPV45 oncoprotein E7 (PDB ID 2EWL), while Apigenin and Apigenin 5-O-Beta-D-Glucopyranoside exhibited significant binding energy against the L1 protein in humans. Similarly, a binding affinity range of - 7.5 kcal/mol to - 8.8 kcal/mol was achieved against DNA polymerase theta, indicating the potential of Apigenin derivatives to inhibit this enzyme (PDB ID 8E23). This finding was further validated through molecular dynamic simulation for 100 ns, analyzing parameters such as RMSD, RMSF, SASA, H-bond, and RoG profiles. The results demonstrated the stability of the selected compounds during the simulation. After passing the stability testing, the compounds underwent screening for ADMET, pharmacokinetics, and drug-likeness properties, fulfilling all the necessary criteria. QSAR, PCA, dynamic cross-correlation matrix, and quantum calculations were conducted, yielding satisfactory outcomes. Since this study utilized in silico computational approaches and obtained outstanding results, further validation is crucial. Therefore, additional wet-lab experiments should be conducted under in vivo and in vitro conditions to confirm the findings.
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Affiliation(s)
- Shopnil Akash
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Birulia, Ashulia, Dhaka, 1216, Bangladesh.
| | - Imren Bayıl
- Department of Bioinformatics and Computational Biology, Gaziantep University, Gaziantep, Turkey
| | - Md Saddam Hossain
- Department of Biomedical Engineering, Faculty of Engineering & Technology, Islamic University, Kushtia, Bangladesh
| | - Md Rezaul Islam
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Birulia, Ashulia, Dhaka, 1216, Bangladesh
| | - Md Eram Hosen
- Professor Joarder DNA and Chromosome Research Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | | | - Hiba-Allah Nafidi
- Department of Food Science, Faculty of Agricultural and Food Sciences, Laval University, 2325, Quebec City, QC, G1V 0A6, Canada
| | - Yousef A Bin Jardan
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Mohammed Bourhia
- Department of Chemistry and Biochemistry, Faculty of Medicine and Pharmacy, Ibn Zohr University, 70000, Laayoune, Morocco
| | - Talha Bin Emran
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School & Legorreta Cancer Center, Brown University, Providence, RI 02912, United States.
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14
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Li L, Liu S, Wang B, Liu F, Xu S, Li P, Chen Y. An Updated Review on Developing Small Molecule Kinase Inhibitors Using Computer-Aided Drug Design Approaches. Int J Mol Sci 2023; 24:13953. [PMID: 37762253 PMCID: PMC10530957 DOI: 10.3390/ijms241813953] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/31/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Small molecule kinase inhibitors (SMKIs) are of heightened interest in the field of drug research and development. There are 79 (as of July 2023) small molecule kinase inhibitors that have been approved by the FDA and hundreds of kinase inhibitor candidates in clinical trials that have shed light on the treatment of some major diseases. As an important strategy in drug design, computer-aided drug design (CADD) plays an indispensable role in the discovery of SMKIs. CADD methods such as docking, molecular dynamic, quantum mechanics/molecular mechanics, pharmacophore, virtual screening, and quantitative structure-activity relationship have been applied to the design and optimization of small molecule kinase inhibitors. In this review, we provide an overview of recent advances in CADD and SMKIs and the application of CADD in the discovery of SMKIs.
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Affiliation(s)
- Linwei Li
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (L.L.); (S.L.); (B.W.); (F.L.); (S.X.)
- Jiangsu Province Engineering Research Center of Eco-Cultivation and High-Value Utilization of Chines Medicinal Materials, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Songtao Liu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (L.L.); (S.L.); (B.W.); (F.L.); (S.X.)
- Jiangsu Province Engineering Research Center of Eco-Cultivation and High-Value Utilization of Chines Medicinal Materials, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
- Key Laboratory of Pesticide, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Bi Wang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (L.L.); (S.L.); (B.W.); (F.L.); (S.X.)
- Jiangsu Province Engineering Research Center of Eco-Cultivation and High-Value Utilization of Chines Medicinal Materials, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Fei Liu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (L.L.); (S.L.); (B.W.); (F.L.); (S.X.)
- Jiangsu Province Engineering Research Center of Eco-Cultivation and High-Value Utilization of Chines Medicinal Materials, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Shu Xu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (L.L.); (S.L.); (B.W.); (F.L.); (S.X.)
- Jiangsu Province Engineering Research Center of Eco-Cultivation and High-Value Utilization of Chines Medicinal Materials, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Pirui Li
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (L.L.); (S.L.); (B.W.); (F.L.); (S.X.)
- Jiangsu Province Engineering Research Center of Eco-Cultivation and High-Value Utilization of Chines Medicinal Materials, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Yu Chen
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (L.L.); (S.L.); (B.W.); (F.L.); (S.X.)
- Jiangsu Province Engineering Research Center of Eco-Cultivation and High-Value Utilization of Chines Medicinal Materials, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
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15
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Ghadirian F, Abbasi H, Bavi O, Naeimabadi A. How living cells are affected during the cold atmospheric pressure plasma treatment. Free Radic Biol Med 2023; 205:141-150. [PMID: 37295538 DOI: 10.1016/j.freeradbiomed.2023.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 06/03/2023] [Accepted: 06/06/2023] [Indexed: 06/12/2023]
Abstract
When the electric discharge process is limited by high voltage electrodes shielding, the ionization measure would be controlled to less than one percent and the temperature to less than 37 °C even at atmospheric pressure, so-called cold atmospheric pressure plasma (CAP). CAP has been found to have profound medical applications in association with its reactive oxygen and nitrogen species (ROS/RNS). In this way that during plasma exposure, the subjected medium (e.g. cell cytoplasmic membrane in plasma therapy) interacts with ROS/RNS. Accordingly, a precise study of the mentioned interactions and their consequences on the cells' behavior changes, is necessary. The results lead to the reduction of possible risks and provide the opportunity of optimizing the efficacy of CAP before the development of CAP applications in the field of plasma medicine. In this report molecular dynamic (MD) simulation is used to investigate the mentioned interactions and a proper and compatible comparison with the experimental results is presented. Based on this, the effects of H2O2, NO and O2 on the living cell's membrane are investigated in biological conditions. Our results show that: i) The hydration of phospholipid polar heads would be enhanced associated with the H2O2 presence. ii) A new definition of the surface area assigned to each phospholipid (APL), more reliable and compatible with the physical expectations, is introduced. iii) The long-term behavior of NO and O2 is their penetration into the lipid bilayer and sometimes passing through the membrane into the cell. The latter would be an indication of internal cells' pathways activation leading to modification of cells' function.
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Affiliation(s)
- Fatemeh Ghadirian
- Faculty of Physics and Energy Engineering, Amirkabir University of Technology, P. O. Box, 15875-4413, Tehran, Iran
| | - Hossein Abbasi
- Faculty of Physics and Energy Engineering, Amirkabir University of Technology, P. O. Box, 15875-4413, Tehran, Iran.
| | - Omid Bavi
- Department of Mechanical Engineering, Shiraz University of Technology, Shiraz, Iran
| | - Aboutorab Naeimabadi
- Faculty of Physics and Energy Engineering, Amirkabir University of Technology, P. O. Box, 15875-4413, Tehran, Iran
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16
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Kciuk M, Marciniak B, Celik I, Zerroug E, Dubey A, Sundaraj R, Mujwar S, Bukowski K, Mojzych M, Kontek R. Pyrazolo[4,3- e]tetrazolo[1,5- b][1,2,4]triazine Sulfonamides as an Important Scaffold for Anticancer Drug Discovery-In Vitro and In Silico Evaluation. Int J Mol Sci 2023; 24:10959. [PMID: 37446136 DOI: 10.3390/ijms241310959] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 06/26/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023] Open
Abstract
Pyrazolo[4,3-e]tetrazolo[1,5-b][1,2,4]triazine sulfonamides (MM-compounds) are a relatively new class of heterocyclic compounds that exhibit a wide variety of biological actions, including anticancer properties. Here, we used caspase enzyme activity assays, flow cytometry analysis of propidium iodide (PI)-stained cells, and a DNA laddering assay to investigate the mechanisms of cell death triggered by the MM-compounds (MM134, -6, -7, and -9). Due to inconsistent results in caspase activity assays, we have performed a bromodeoxyuridine (BrdU) incorporation assay, colony formation assay, and gene expression profiling. The compounds' cytotoxic and pro-oxidative properties were also assessed. Additionally, computational studies were performed to demonstrate the potential of the scaffold for future drug discovery endeavors. MM-compounds exhibited strong micromolar (0.06-0.35 µM) anti-proliferative and pro-oxidative activity in two cancer cell lines (BxPC-3 and PC-3). Activation of caspase 3/7 was observed following a 24-h treatment of BxPC-3 cells with IC50 concentrations of MM134, -6, and -9 compounds. However, no DNA fragmentation characteristics for apoptosis were observed in the flow cytometry and DNA laddering analysis. Gene expression data indicated up-regulation of BCL10, GADD45A, RIPK2, TNF, TNFRSF10B, and TNFRSF1A (TNF-R1) following treatment of cells with the MM134 compound. Moreover, in silico studies indicated AKT2 kinase as the primary target of compounds. MM-compounds exhibit strong cytotoxic activity with pro-oxidative, pro-apoptotic, and possibly pro-necroptotic properties that could be employed for further drug discovery approaches.
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Affiliation(s)
- Mateusz Kciuk
- Department of Molecular Biotechnology and Genetics, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland
- Doctoral School of Exact and Natural Sciences, University of Lodz, Banacha Street 12/16, 90-237 Lodz, Poland
| | - Beata Marciniak
- Department of Molecular Biotechnology and Genetics, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland
| | - Ismail Celik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University, Kayseri 38280, Turkey
| | - Enfale Zerroug
- Group of Computational and Pharmaceutical Chemistry, LMCE Laboratory, University of Biskra, BP 145, Biskra 07000, Algeria
| | - Amit Dubey
- Computational Chemistry and Drug Discovery Division, Quanta Calculus, Greater Noida 274203, Uttar Prades, India
- Department of Pharmacology, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai 602105, Tamil Nadu, India
| | - Rajamanikandan Sundaraj
- Centre for Drug Discovery, Department of Biochemistry, Karpagam Academy of Higher Education, Coimbatore 641021, Tamil Nadu, India
| | - Somdutt Mujwar
- Chitkara College of Pharmacy, Chitkara University, Rajpura 140401, Punjab, India
| | - Karol Bukowski
- Department of Molecular Biotechnology and Genetics, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland
| | - Mariusz Mojzych
- Department of Chemistry, Siedlce University of Natural Sciences and Humanities, 3 Maja 54, 08-110 Siedlce, Poland
| | - Renata Kontek
- Department of Molecular Biotechnology and Genetics, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland
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17
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Nada H, Elkamhawy A, Lee K. Identification of 1H-purine-2,6-dione derivative as a potential SARS-CoV-2 main protease inhibitor: molecular docking, dynamic simulations, and energy calculations. PeerJ 2022; 10:e14120. [PMID: 36225900 PMCID: PMC9549888 DOI: 10.7717/peerj.14120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 09/05/2022] [Indexed: 01/25/2023] Open
Abstract
The rapid spread of the coronavirus since its first appearance in 2019 has taken the world by surprise, challenging the global economy, and putting pressure on healthcare systems across the world. The introduction of preventive vaccines only managed to slow the rising death rates worldwide, illuminating the pressing need for developing effective antiviral therapeutics. The traditional route of drug discovery has been known to require years which the world does not currently have. In silico approaches in drug design have shown promising results over the last decade, helping to decrease the required time for drug development. One of the vital non-structural proteins that are essential to viral replication and transcription is the SARS-CoV-2 main protease (Mpro). Herein, using a test set of recently identified COVID-19 inhibitors, a pharmacophore was developed to screen 20 million drug-like compounds obtained from a freely accessible Zinc database. The generated hits were ranked using a structure based virtual screening technique (SBVS), and the top hits were subjected to in-depth molecular docking studies and MM-GBSA calculations over SARS-COV-2 Mpro. Finally, the most promising hit, compound (1), and the potent standard (III) were subjected to 100 ns molecular dynamics (MD) simulations and in silico ADME study. The result of the MD analysis as well as the in silico pharmacokinetic study reveal compound 1 to be a promising SARS-Cov-2 MPro inhibitor suitable for further development.
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Affiliation(s)
- Hossam Nada
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, South Korea,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Badr University in Cairo, Cairo, Egypt
| | - Ahmed Elkamhawy
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, South Korea,Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Kyeong Lee
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, South Korea
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18
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Ilaghi-Hoseini S, Garkani-Nejad Z. Research and study of 2-((4,6 dimethyl pyrimidine-2-yle) thio)-N-phenyl acetamide derivatives as inhibitors of sirtuin 2 protein for the treatment of cancer using QSAR, molecular docking and molecular dynamic simulation. J Mol Model 2022; 28:343. [PMID: 36198913 DOI: 10.1007/s00894-022-05288-4] [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: 02/05/2022] [Accepted: 08/19/2022] [Indexed: 10/10/2022]
Abstract
Phenyl acetamide derivatives have a wide range of biological activities, so their research and development can be useful and effective for the design production of new drugs. In this project, quantitative structure-activity relationship (QSAR) was performed. For modeling two methods of multiple linear regression (MLR) and nonlinear regression of support vector machine (SVR) were used. In the MLR stage, the best model with the values of R2train = 0.913 and R2test = 0.881 was selected by stepwise method. In this model, 4 descriptors of BELV2, GATS8p, GATS6e and RDF080m were included, which were used as input for the nonlinear support vector regression method. In the SVR model, the best results were obtained using the radial Gaussian kernel function (RBF) with R2train = 0.978 and R2test = 0.990. In the next step, using molecular docking and molecular dynamic simulation methods, the interaction between phenyl acetamide derivatives and the sirtuin 2 protein was investigated. Examining the results of molecular docking, it was observed that these derivatives formed complexes by forming hydrogen and hydrophobic bonds with the sirtuin 2 protein. Also, the results of molecular dynamic simulation show that phenyl acetamide compounds form stable complex with the sirtuin 2 protein, and it was found that the compounds with more activity have formed a number of hydrogen bonds with the protein.
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Affiliation(s)
- Sahar Ilaghi-Hoseini
- Chemistry Department, Faculty of Science, Shahid Bahonar University of Kerman, Kerman, Iran.,Young Researchers Society, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Zahra Garkani-Nejad
- Chemistry Department, Faculty of Science, Shahid Bahonar University of Kerman, Kerman, Iran.
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19
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Dudas B, Decleves X, Cisternino S, Perahia D, Miteva M. ABCG2/BCRP transport mechanism revealed through kinetically excited targeted molecular dynamics simulations. Comput Struct Biotechnol J 2022; 20:4195-4205. [PMID: 36016719 PMCID: PMC9389183 DOI: 10.1016/j.csbj.2022.07.035] [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: 05/20/2022] [Revised: 07/21/2022] [Accepted: 07/21/2022] [Indexed: 12/03/2022] Open
Abstract
ABCG2/BCRP is an ABC transporter that plays an important role in tissue protection by exporting endogenous substrates and xenobiotics. ABCG2 is of major interest due to its involvement in multidrug resistance (MDR), and understanding its complex efflux mechanism is essential to preventing MDR and drug-drug interactions (DDI). ABCG2 export is characterized by two major conformational transitions between inward- and outward-facing states, the structures of which have been resolved. Yet, the entire transport cycle has not been characterized to date. Our study bridges the gap between the two extreme conformations by studying connecting pathways. We developed an innovative approach to enhance molecular dynamics simulations, ‘kinetically excited targeted molecular dynamics’, and successfully simulated the transitions between inward- and outward-facing states in both directions and the transport of the endogenous substrate estrone 3-sulfate. We discovered an additional pocket between the two substrate-binding cavities and found that the presence of the substrate in the first cavity is essential to couple the movements between the nucleotide-binding and transmembrane domains. Our study shed new light on the complex efflux mechanism, and we provided transition pathways that can help to identify novel substrates and inhibitors of ABCG2 and probe new drug candidates for MDR and DDI.
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20
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Mtemeli FL, Ndlovu J, Mugumbate G, Makwikwi T, Shoko R. Advances in schistosomiasis drug discovery based on natural products. ALL LIFE 2022. [DOI: 10.1080/26895293.2022.2080281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- F. L. Mtemeli
- Department of Biology, School of Natural Sciences and Mathematics Chinhoyi University of Technology, Chinhoyi, Zimbabwe
| | - J. Ndlovu
- Department of Biology, School of Natural Sciences and Mathematics Chinhoyi University of Technology, Chinhoyi, Zimbabwe
| | - G. Mugumbate
- Department of Chemical Technology, Midlands State University, Gweru, Zimbabwe
| | - T. Makwikwi
- Department of Pharmaceutical Sciences, Tshwane University of Technology, Pretoria, South Africa
| | - R. Shoko
- Department of Biology, School of Natural Sciences and Mathematics Chinhoyi University of Technology, Chinhoyi, Zimbabwe
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21
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Roy RK, Patra N. Prediction of COMT Inhibitors Using Machine Learning and Molecular Dynamics Methods. J Phys Chem B 2022; 126:3477-3492. [PMID: 35533359 DOI: 10.1021/acs.jpcb.1c10278] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Catechol O-methyltransferase (COMT) plays a vital role in deactivating neurotransmitters like dopamine, norepinephrine, etc., by methylating those compounds. However, the deactivation of an excess amount of neurotransmitters leads to serious mental ailments such as Parkinson's disease. Molecules that bind inside the enzyme's active site inhibit this methylation mechanism by methylating themselves, termed COMT inhibitors. Our study is focused on designing these inhibitors by various machine learning methods. First, we have developed a classification model with experimentally available COMT inhibitors, which helped us generate a new data set of small inhibitor-like molecules. Then, to predict the activity of the new molecules, we have applied regression techniques such as Random Forest, AdaBoost, gradient boosting, and support vector machines. Each of the regression models yielded an R2 value > 70% for both training and test data sets. Finally, to validate our models, 200 ns long molecular dynamics (MD) simulations of the two known inhibitors with known IC50 values and the resultant inhibitors were performed inside the binding pockets to check their stability within. The free energy barrier of the methyl transfer from S-adenosyl-l-methionine (SAM) to each inhibitor was determined by combining steered molecular dynamics (SMD) and umbrella sampling using the quantum mechanics/molecular mechanics (QM/MM) method.
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Affiliation(s)
- Rakesh Kumar Roy
- Department of Chemistry & Chemical Biology, Indian Institute of Technology (ISM) Dhanbad, Dhanbad 826004, India
| | - Niladri Patra
- Department of Chemistry & Chemical Biology, Indian Institute of Technology (ISM) Dhanbad, Dhanbad 826004, India
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22
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Sydow D, Rodríguez-Guerra J, Kimber TB, Schaller D, Taylor CJ, Chen Y, Leja M, Misra S, Wichmann M, Ariamajd A, Volkamer A. TeachOpenCADD 2022: open source and FAIR Python pipelines to assist in structural bioinformatics and cheminformatics research. Nucleic Acids Res 2022; 50:W753-W760. [PMID: 35524571 PMCID: PMC9252772 DOI: 10.1093/nar/gkac267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 03/30/2022] [Accepted: 04/06/2022] [Indexed: 11/18/2022] Open
Abstract
Computational pipelines have become a crucial part of modern drug discovery campaigns. Setting up and maintaining such pipelines, however, can be challenging and time-consuming—especially for novice scientists in this domain. TeachOpenCADD is a platform that aims to teach domain-specific skills and to provide pipeline templates as starting points for research projects. We offer Python-based solutions for common tasks in cheminformatics and structural bioinformatics in the form of Jupyter notebooks, based on open source resources only. Including the 12 newly released additions, TeachOpenCADD now contains 22 notebooks that cover both theoretical background as well as hands-on programming. To promote reproducible and reusable research, we apply software best practices to our notebooks such as testing with automated continuous integration and adhering to the idiomatic Python style. The new TeachOpenCADD website is available at https://projects.volkamerlab.org/teachopencadd and all code is deposited on GitHub.
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Affiliation(s)
- Dominique Sydow
- In Silico Toxicology and Structural Bioinformatics, Institute of Physiology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Germany
| | - Jaime Rodríguez-Guerra
- In Silico Toxicology and Structural Bioinformatics, Institute of Physiology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Germany
| | - Talia B Kimber
- In Silico Toxicology and Structural Bioinformatics, Institute of Physiology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Germany
| | - David Schaller
- In Silico Toxicology and Structural Bioinformatics, Institute of Physiology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Germany
| | - Corey J Taylor
- In Silico Toxicology and Structural Bioinformatics, Institute of Physiology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Germany
| | - Yonghui Chen
- In Silico Toxicology and Structural Bioinformatics, Institute of Physiology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Germany
| | - Mareike Leja
- In Silico Toxicology and Structural Bioinformatics, Institute of Physiology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Germany
| | - Sakshi Misra
- In Silico Toxicology and Structural Bioinformatics, Institute of Physiology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Germany
| | - Michele Wichmann
- In Silico Toxicology and Structural Bioinformatics, Institute of Physiology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Germany
| | - Armin Ariamajd
- In Silico Toxicology and Structural Bioinformatics, Institute of Physiology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Germany
| | - Andrea Volkamer
- In Silico Toxicology and Structural Bioinformatics, Institute of Physiology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Germany
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23
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Design, Synthesis and Evaluation of Fused Bicyclo[2.2.2]octene as a Potential Core Scaffold for the Non-Covalent Inhibitors of SARS-CoV-2 3CLpro Main Protease. Pharmaceuticals (Basel) 2022; 15:ph15050539. [PMID: 35631364 PMCID: PMC9145702 DOI: 10.3390/ph15050539] [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: 04/06/2022] [Revised: 04/22/2022] [Accepted: 04/24/2022] [Indexed: 12/22/2022] Open
Abstract
The emergence of SARS-CoV-2, responsible for the global COVID-19 pandemic, requires the rapid development of novel antiviral drugs that would contribute to an effective treatment alongside vaccines. Drug repurposing and development of new molecules targeting numerous viral targets have already led to promising drug candidates. To this end, versatile molecular scaffolds with high functionalization capabilities play a key role. Starting with the clinically used conformationally flexible HIV-1 protease inhibitors that inhibit replication of SARS-CoV-2 and bind major protease 3CLpro, we designed and synthesized a series of rigid bicyclo[2.2.2]octenes fused to N-substituted succinimides to test whether this core scaffold could support the development of non-covalent 3CLpro inhibitors. Inhibition assays confirmed that some compounds can inhibit the SARS-CoV-2 main protease; the most promising compound 11a inhibited 3CLpro in micromolar range (IC50 = 102.2 μM). Molecular simulations of the target-ligand complex in conjunction with dynophore analyses and endpoint free energy calculations provide additional insight and first recommendations for future optimization. The fused bicyclo[2.2.2]octenes can be used as a new potential starting point in the development of non-covalent SARS-CoV-2 3CLpro protease inhibitors and the study also substantiates the potential of this versatile scaffold for the development of biologically active molecules.
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24
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Multi spectroscopy and molecular modeling aspects related to drug interaction of aspirin with alpha chymotrypsin; structural change and protease activity. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.118698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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25
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Kim JS, Arango AS, Shah S, Arnold WR, Tajkhorshid E, Das A. Anthracycline derivatives inhibit cardiac CYP2J2. J Inorg Biochem 2022; 229:111722. [PMID: 35078036 PMCID: PMC8860876 DOI: 10.1016/j.jinorgbio.2022.111722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 01/05/2022] [Accepted: 01/06/2022] [Indexed: 11/20/2022]
Abstract
Anthracycline chemotherapeutics are highly effective, but their clinical usefulness is hampered by adverse side effects such as cardiotoxicity. Cytochrome P450 2J2 (CYP2J2) is a cytochrome P450 epoxygenase in human cardiomyocytes that converts arachidonic acid (AA) to cardioprotective epoxyeicosatrienoic acid (EET) regioisomers. Herein, we performed biochemical studies to understand the interaction of anthracycline derivatives (daunorubicin, doxorubicin, epirubicin, idarubicin, 5-iminodaunorubicin, zorubicin, valrubicin, and aclarubicin) with CYP2J2. We utilized fluorescence polarization (FP) to assess whether anthracyclines bind to CYP2J2. We found that aclarubicin bound the strongest to CYP2J2 despite it having large bulky groups. We determined that ebastine competitively inhibits anthracycline binding, suggesting that ebastine and anthracyclines may share the same binding site. Molecular dynamics and ensemble docking revealed electrostatic interactions between the anthracyclines and CYP2J2, contributing to binding stability. In particular, the glycosamine groups in anthracyclines are stabilized by binding to glutamate and aspartate residues in CYP2J2 forming salt bridge interactions. Furthermore, we used iterative ensemble docking schemes to gauge anthracycline influence on EET regioisomer production and anthracycline inhibition on AA metabolism. This was followed by experimental validation of CYP2J2-mediated metabolism of anthracycline derivatives using liquid chromatography tandem mass spectrometry fragmentation analysis and inhibition of CYP2J2-mediated AA metabolism by these derivatives. Taken together, we use both experimental and theoretical methodologies to unveil the interactions of anthracycline derivatives with CYP2J2. These studies will help identify alternative mechanisms of how anthracycline cardiotoxicity may be mediated through the inhibition of cardiac P450, which will aid in the design of new anthracycline derivatives with lower toxicity.
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Affiliation(s)
- Justin S Kim
- Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States of America
| | - Andres S Arango
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States of America; Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States of America
| | - Swapnil Shah
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States of America
| | - William R Arnold
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States of America
| | - Emad Tajkhorshid
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States of America; Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States of America; Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States of America; Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States of America
| | - Aditi Das
- Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States of America; Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States of America; Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States of America; Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States of America; Department of Comparative Biosciences, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States of America.
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26
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Basciu A, Callea L, Motta S, Bonvin AM, Bonati L, Vargiu AV. No dance, no partner! A tale of receptor flexibility in docking and virtual screening. VIRTUAL SCREENING AND DRUG DOCKING 2022. [DOI: 10.1016/bs.armc.2022.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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27
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González-Fernández C, Bringas E, Oostenbrink C, Ortiz I. In silico investigation and surmounting of Lipopolysaccharide barrier in Gram-Negative Bacteria: How far has molecular dynamics Come? Comput Struct Biotechnol J 2022; 20:5886-5901. [PMID: 36382192 PMCID: PMC9636410 DOI: 10.1016/j.csbj.2022.10.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/24/2022] [Accepted: 10/24/2022] [Indexed: 11/29/2022] Open
Abstract
Lipopolysaccharide (LPS), a main component of the outer membrane of Gram-negative bacteria, has crucial implications on both antibiotic resistance and the overstimulation of the host innate immune system. Fighting against these global concerns calls for the molecular understanding of the barrier function and immunostimulatory ability of LPS. Molecular dynamics (MD) simulations have become an invaluable tool for uncovering important findings in LPS research. While the reach of MD simulations for investigating the immunostimulatory ability of LPS has been already outlined, little attention has been paid to the role of MD simulations for exploring its barrier function and synthesis. Herein, we give an overview about the impact of MD simulations on gaining insight into the shield role and synthesis pathway of LPS, which have attracted considerable attention to discover molecules able to surmount antibiotic resistance, either circumventing LPS defenses or disrupting its synthesis. We specifically focus on the enhanced sampling and free energy calculation methods that have been combined with MD simulations to address such research. We also highlight the use of special-purpose MD supercomputers, the importance of appropriate LPS and ions parameterization to obtain reliable results, and the complementary views that MD and wet-lab experiments provide. Thereby, this work, which covers the last five years of research, apart from outlining the phenomena and strategies that are being explored, evidences the valuable insights that are gained by MD, which may be useful to advance antibiotic design, and what the prospects of this in silico method could be in LPS research.
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Affiliation(s)
- Cristina González-Fernández
- Department of Chemical and Biomolecular Engineering, ETSIIT, University of Cantabria, Avda. Los Castros s/n, 39005 Santander, Spain
| | - Eugenio Bringas
- Department of Chemical and Biomolecular Engineering, ETSIIT, University of Cantabria, Avda. Los Castros s/n, 39005 Santander, Spain
| | - Chris Oostenbrink
- Institute for Molecular Modeling and Simulation, BOKU – University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Inmaculada Ortiz
- Department of Chemical and Biomolecular Engineering, ETSIIT, University of Cantabria, Avda. Los Castros s/n, 39005 Santander, Spain
- Corresponding author.
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28
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Janežič M, Valjavec K, Loboda KB, Herlah B, Ogris I, Kozorog M, Podobnik M, Grdadolnik SG, Wolber G, Perdih A. Dynophore-Based Approach in Virtual Screening: A Case of Human DNA Topoisomerase IIα. Int J Mol Sci 2021; 22:ijms222413474. [PMID: 34948269 PMCID: PMC8703789 DOI: 10.3390/ijms222413474] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/23/2021] [Accepted: 12/10/2021] [Indexed: 12/04/2022] Open
Abstract
In this study, we utilized human DNA topoisomerase IIα as a model target to outline a dynophore-based approach to catalytic inhibitor design. Based on MD simulations of a known catalytic inhibitor and the native ATP ligand analog, AMP-PNP, we derived a joint dynophore model that supplements the static structure-based-pharmacophore information with a dynamic component. Subsequently, derived pharmacophore models were employed in a virtual screening campaign of a library of natural compounds. Experimental evaluation identified flavonoid compounds with promising topoisomerase IIα catalytic inhibition and binding studies confirmed interaction with the ATPase domain. We constructed a binding model through docking and extensively investigated it with molecular dynamics MD simulations, essential dynamics, and MM-GBSA free energy calculations, thus reconnecting the new results to the initial dynophore-based screening model. We not only demonstrate a new design strategy that incorporates a dynamic component of molecular recognition, but also highlight new derivates in the established flavonoid class of topoisomerase II inhibitors.
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Affiliation(s)
- Matej Janežič
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia; (M.J.); (K.V.); (K.B.L.); (B.H.); (I.O.); (M.K.); (M.P.); (S.G.G.)
- Laboratory for Structural Bioinformatics, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Katja Valjavec
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia; (M.J.); (K.V.); (K.B.L.); (B.H.); (I.O.); (M.K.); (M.P.); (S.G.G.)
| | - Kaja Bergant Loboda
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia; (M.J.); (K.V.); (K.B.L.); (B.H.); (I.O.); (M.K.); (M.P.); (S.G.G.)
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia
| | - Barbara Herlah
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia; (M.J.); (K.V.); (K.B.L.); (B.H.); (I.O.); (M.K.); (M.P.); (S.G.G.)
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia
| | - Iza Ogris
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia; (M.J.); (K.V.); (K.B.L.); (B.H.); (I.O.); (M.K.); (M.P.); (S.G.G.)
- Faculty of Medicine, University of Ljubljana, Vrazov trg 2, SI-1000 Ljubljana, Slovenia
| | - Mirijam Kozorog
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia; (M.J.); (K.V.); (K.B.L.); (B.H.); (I.O.); (M.K.); (M.P.); (S.G.G.)
| | - Marjetka Podobnik
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia; (M.J.); (K.V.); (K.B.L.); (B.H.); (I.O.); (M.K.); (M.P.); (S.G.G.)
| | - Simona Golič Grdadolnik
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia; (M.J.); (K.V.); (K.B.L.); (B.H.); (I.O.); (M.K.); (M.P.); (S.G.G.)
| | - Gerhard Wolber
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Straße 2-4, 14195 Berlin, Germany;
| | - Andrej Perdih
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia; (M.J.); (K.V.); (K.B.L.); (B.H.); (I.O.); (M.K.); (M.P.); (S.G.G.)
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia
- Correspondence: ; Tel.: +386-1-4760-376
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29
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Integrated computer-aided formulation design: A case study of andrographolide/ cyclodextrin ternary formulation. Asian J Pharm Sci 2021; 16:494-507. [PMID: 34703498 PMCID: PMC8520056 DOI: 10.1016/j.ajps.2021.03.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 02/28/2021] [Accepted: 03/21/2021] [Indexed: 01/17/2023] Open
Abstract
Current formulation development strongly relies on trial-and-error experiments in the laboratory by pharmaceutical scientists, which is time-consuming, high cost and waste materials. This research aims to integrate various computational tools, including machine learning, molecular dynamic simulation and physiologically based absorption modeling (PBAM), to enhance andrographolide (AG) /cyclodextrins (CDs) formulation design. The lightGBM prediction model we built before was utilized to predict AG/CDs inclusion's binding free energy. AG/γ-CD inclusion complexes showed the strongest binding affinity, which was experimentally validated by the phase solubility study. The molecular dynamic simulation was used to investigate the inclusion mechanism between AG and γ-CD, which was experimentally characterized by DSC, FTIR and NMR techniques. PBAM was applied to simulate the in vivo behavior of the formulations, which were validated by cell and animal experiments. Cell experiments revealed that the presence of D-α-Tocopherol polyethylene glycol succinate (TPGS) significantly increased the intracellular uptake of AG in MDCK-MDR1 cells and the absorptive transport of AG in MDCK-MDR1 monolayers. The relative bioavailability of the AG-CD-TPGS ternary system in rats was increased to 2.6-fold and 1.59-fold compared with crude AG and commercial dropping pills, respectively. In conclusion, this is the first time to integrate various computational tools to develop a new AG-CD-TPGS ternary formulation with significant improvement of aqueous solubility, dissolution rate and bioavailability. The integrated computational tool is a novel and robust methodology to facilitate pharmaceutical formulation design.
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30
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González-Fernández C, Basauri A, Fallanza M, Bringas E, Oostenbrink C, Ortiz I. Fighting Against Bacterial Lipopolysaccharide-Caused Infections through Molecular Dynamics Simulations: A Review. J Chem Inf Model 2021; 61:4839-4851. [PMID: 34559524 PMCID: PMC8549069 DOI: 10.1021/acs.jcim.1c00613] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
![]()
Lipopolysaccharide
(LPS) is the primary component of the outer
leaflet of Gram-negative bacterial outer membranes. LPS elicits an
overwhelming immune response during infection, which can lead to life-threatening
sepsis or septic shock for which no suitable treatment is available
so far. As a result of the worldwide expanding multidrug-resistant
bacteria, the occurrence and frequency of sepsis are expected to increase;
thus, there is an urge to develop novel strategies for treating bacterial
infections. In this regard, gaining an in-depth understanding about
the ability of LPS to both stimulate the host immune system and interact
with several molecules is crucial for fighting against LPS-caused
infections and allowing for the rational design of novel antisepsis
drugs, vaccines and LPS sequestration and detection methods. Molecular
dynamics (MD) simulations, which are understood as being a computational
microscope, have proven to be of significant value to understand LPS-related
phenomena, driving and optimizing experimental research studies. In
this work, a comprehensive review on the methods that can be combined
with MD simulations, recently applied in LPS research, is provided.
We focus especially on both enhanced sampling methods, which enable
the exploration of more complex systems and access to larger time
scales, and free energy calculation approaches. Thereby, apart from
outlining several strategies for surmounting LPS-caused infections,
this work reports the current state-of-the-art of the methods applied
with MD simulations for moving a step forward in the development of
such strategies.
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Affiliation(s)
- Cristina González-Fernández
- Department of Chemical and Biomolecular Engineering, ETSIIT, University of Cantabria, Avda. Los Castros s/n, 39005 Santander, Spain
| | - Arantza Basauri
- Department of Chemical and Biomolecular Engineering, ETSIIT, University of Cantabria, Avda. Los Castros s/n, 39005 Santander, Spain
| | - Marcos Fallanza
- Department of Chemical and Biomolecular Engineering, ETSIIT, University of Cantabria, Avda. Los Castros s/n, 39005 Santander, Spain
| | - Eugenio Bringas
- Department of Chemical and Biomolecular Engineering, ETSIIT, University of Cantabria, Avda. Los Castros s/n, 39005 Santander, Spain
| | - Chris Oostenbrink
- Institute for Molecular Modeling and Simulation, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Inmaculada Ortiz
- Department of Chemical and Biomolecular Engineering, ETSIIT, University of Cantabria, Avda. Los Castros s/n, 39005 Santander, Spain
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31
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Kapon Y, Saha A, Duanis-Assaf T, Stuyver T, Ziv A, Metzger T, Yochelis S, Shaik S, Naaman R, Reches M, Paltiel Y. Evidence for new enantiospecific interaction force in chiral biomolecules. Chem 2021. [DOI: 10.1016/j.chempr.2021.08.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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32
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Lee JY, Lee K, Koh B. Identification of new IL-7Rα small-molecule agonists: a multi-computational approach. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2021; 32:719-729. [PMID: 34431428 DOI: 10.1080/1062936x.2021.1969684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 08/15/2021] [Indexed: 06/13/2023]
Abstract
Interleukin 7 (IL-7) is an essential cytokine that acts as a potent growth factor of T-cells and supports the growth of B-cell precursors. IL-7 binds to a heterodimeric receptor consisting of an IL-7 receptor alpha (IL-7Rα) and the common gamma chain receptor (γc) which is shared with IL-2, IL-4, IL-9, IL-15 and IL-21. The discovery of small-molecule agonists of cytokines would be of great pharmaceutical interest with the increasing scientific rationale. In this study, a series of molecular modelling methods, including field-based pharmacophore virtual screening, protein-protein docking and molecular dynamics simulations, led to the identification of two compounds (i.e. 1 and 2) of different classes that exhibit enhanced agonistic effects by activating the IL-7 signalling cascade. One of these compounds was selected as a hit and represents the first small-molecule agonist of IL-7Rα with single-digit micromolar activity. Moreover, the prediction model of the active compound to the IL-7Rα/γc interaction complex provides insight into the binding of a small-molecule agonist to its receptor.
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Affiliation(s)
- J-Y Lee
- Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
| | - K Lee
- Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
| | - B Koh
- Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
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33
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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.
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Affiliation(s)
- Anderson A E Santo
- Institute of Chemistry, São Paulo State University, Araraquara, SP, Brazil
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34
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Dudas B, Toth D, Perahia D, Nicot AB, Balog E, Miteva MA. Insights into the substrate binding mechanism of SULT1A1 through molecular dynamics with excited normal modes simulations. Sci Rep 2021; 11:13129. [PMID: 34162941 PMCID: PMC8222352 DOI: 10.1038/s41598-021-92480-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 06/10/2021] [Indexed: 11/14/2022] Open
Abstract
Sulfotransferases (SULTs) are phase II drug-metabolizing enzymes catalyzing the sulfoconjugation from the co-factor 3′-phosphoadenosine 5′-phosphosulfate (PAPS) to a substrate. It has been previously suggested that a considerable shift of SULT structure caused by PAPS binding could control the capability of SULT to bind large substrates. We employed molecular dynamics (MD) simulations and the recently developed approach of MD with excited normal modes (MDeNM) to elucidate molecular mechanisms guiding the recognition of diverse substrates and inhibitors by SULT1A1. MDeNM allowed exploring an extended conformational space of PAPS-bound SULT1A1, which has not been achieved up to now by using classical MD. The generated ensembles combined with docking of 132 SULT1A1 ligands shed new light on substrate and inhibitor binding mechanisms. Unexpectedly, our simulations and analyses on binding of the substrates estradiol and fulvestrant demonstrated that large conformational changes of the PAPS-bound SULT1A1 could occur independently of the co-factor movements that could be sufficient to accommodate large substrates as fulvestrant. Such structural displacements detected by the MDeNM simulations in the presence of the co-factor suggest that a wider range of drugs could be recognized by PAPS-bound SULT1A1 and highlight the utility of including MDeNM in protein–ligand interactions studies where major rearrangements are expected.
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Affiliation(s)
- Balint Dudas
- Inserm U1268 MCTR, CiTCoM UMR 8038 CNRS - University of Paris, Pharmacy Faculty of Paris, Paris, France.,Laboratoire de Biologie et Pharmacologie Appliquée, Ecole Normale Supérieure Paris-Saclay, UMR 8113, CNRS, Gif-sur-Yvette, France
| | - Daniel Toth
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - David Perahia
- Laboratoire de Biologie et Pharmacologie Appliquée, Ecole Normale Supérieure Paris-Saclay, UMR 8113, CNRS, Gif-sur-Yvette, France
| | - Arnaud B Nicot
- Inserm, Université de Nantes, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, 44000, Nantes, France
| | - Erika Balog
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary.
| | - Maria A Miteva
- Inserm U1268 MCTR, CiTCoM UMR 8038 CNRS - University of Paris, Pharmacy Faculty of Paris, Paris, France.
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35
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Gediz Erturk A, Sahin A, Bati Ay E, Pelit E, Bagdatli E, Kulu I, Gul M, Mesci S, Eryilmaz S, Oba Ilter S, Yildirim T. A Multidisciplinary Approach to Coronavirus Disease (COVID-19). Molecules 2021; 26:3526. [PMID: 34207756 PMCID: PMC8228528 DOI: 10.3390/molecules26123526] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/04/2021] [Accepted: 06/04/2021] [Indexed: 02/07/2023] Open
Abstract
Since December 2019, humanity has faced an important global threat. Many studies have been published on the origin, structure, and mechanism of action of the SARS-CoV-2 virus and the treatment of its disease. The priority of scientists all over the world has been to direct their time to research this subject. In this review, we highlight chemical studies and therapeutic approaches to overcome COVID-19 with seven different sections. These sections are the structure and mechanism of action of SARS-CoV-2, immunotherapy and vaccine, computer-aided drug design, repurposing therapeutics for COVID-19, synthesis of new molecular structures against COVID-19, food safety/security and functional food components, and potential natural products against COVID-19. In this work, we aimed to screen all the newly synthesized compounds, repurposing chemicals covering antiviral, anti-inflammatory, antibacterial, antiparasitic, anticancer, antipsychotic, and antihistamine compounds against COVID-19. We also highlight computer-aided approaches to develop an anti-COVID-19 molecule. We explain that some phytochemicals and dietary supplements have been identified as antiviral bioproducts, which have almost been successfully tested against COVID-19. In addition, we present immunotherapy types, targets, immunotherapy and inflammation/mutations of the virus, immune response, and vaccine issues.
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Affiliation(s)
- Aliye Gediz Erturk
- Department of Chemistry, Faculty of Arts and Sciences, Ordu University, Altınordu, Ordu 52200, Turkey;
| | - Arzu Sahin
- Department of Basic Medical Sciences—Physiology, Faculty of Medicine, Uşak University, 1-EylulUşak 64000, Turkey;
| | - Ebru Bati Ay
- Department of Plant and Animal Production, Suluova Vocational School, Amasya University, Suluova, Amasya 05100, Turkey;
| | - Emel Pelit
- Department of Chemistry, Faculty of Arts and Sciences, Kırklareli University, Kırklareli 39000, Turkey;
| | - Emine Bagdatli
- Department of Chemistry, Faculty of Arts and Sciences, Ordu University, Altınordu, Ordu 52200, Turkey;
| | - Irem Kulu
- Department of Chemistry, Faculty of Basic Sciences, Gebze Technical University, Kocaeli 41400, Turkey;
| | - Melek Gul
- Department of Chemistry, Faculty of Arts and Sciences, Amasya University, Ipekkoy, Amasya 05100, Turkey
| | - Seda Mesci
- Scientific Technical Application and Research Center, Hitit University, Çorum 19030, Turkey;
| | - Serpil Eryilmaz
- Department of Physics, Faculty of Arts and Sciences, Amasya University, Ipekkoy, Amasya 05100, Turkey;
| | - Sirin Oba Ilter
- Food Processing Department, Suluova Vocational School, Amasya University, Suluova, Amasya 05100, Turkey;
| | - Tuba Yildirim
- Department of Biology, Faculty of Arts and Sciences, Amasya University, Ipekkoy, Amasya 05100, Turkey;
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36
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Haghshenas H, Kaviani B, Firouzeh M, Tavakol H. Developing a variation of 3D-QSAR/MD method in drug design. J Comput Chem 2021; 42:917-929. [PMID: 33719136 DOI: 10.1002/jcc.26514] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 02/22/2021] [Accepted: 02/26/2021] [Indexed: 12/22/2022]
Abstract
In continuation of the previous reports on a combination of 3D-quantitative structure-activity relationships (QSAR) with computational molecular dynamics (MD) studies, a new variation of 3D-QSAR/MD method has been employed for drug-design as an alternative or supplementary for the typical experimental methods. The presented method is more cost-effective and less time-consuming than the previous methods and avoids several restrictions of experimental methods, such as validity estimation, and predictability. For this purpose, seven inhibitors for bromodomain (BRD)-containing protein, as an important protein in the development of different types of cancer and responsible for oncogenic rearrangements, have been selected to study of their interactions by docking and MD simulations using molecular mechanics/generalized born surface area (MM/GBSA) method. To build the proposed model, a common variant of 3D-QSAR methods, comparative molecular field analysis has been employed using a dataset of 100 MD-extracted ligand conformations and their corresponding MM/GBSA BRD4-binding energies. The results showed excellent predictability of the generated model for both the training set and test groups. Finally, two new inhibitors were selected among total 4000 designed derivatives (generated through evolutionary techniques) using the proposed 3D-QSAR-MD model. The potentials of these inhibitors were assessed by MD simulations, which showed the higher inhibitory of these compounds than the previous inhibitors. Therefore, this method showed high potentials for acceleration of the procedure of drug design and a basis for joining researchers in computational biology and pharmaceutical sciences.
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Affiliation(s)
- Hamed Haghshenas
- Division of Biochemistry, Department of Biology, Faculty of Sciences, Shahrekord University, Shahrekord, Iran
| | - Bita Kaviani
- Division of Genetics, Department of Biology, Faculty of Sciences, Islamic Azad University, Shahrekord, Iran
| | - Monireh Firouzeh
- Department of Nanobiotechnology, NourDanesh Institute of Higher Education, Isfahan, Iran
| | - Hossein Tavakol
- Department of Chemistry, Isfahan University of Technology, Isfahan, Iran
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37
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Morawietz T, Artrith N. Machine learning-accelerated quantum mechanics-based atomistic simulations for industrial applications. J Comput Aided Mol Des 2021; 35:557-586. [PMID: 33034008 PMCID: PMC8018928 DOI: 10.1007/s10822-020-00346-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 09/26/2020] [Indexed: 01/13/2023]
Abstract
Atomistic simulations have become an invaluable tool for industrial applications ranging from the optimization of protein-ligand interactions for drug discovery to the design of new materials for energy applications. Here we review recent advances in the use of machine learning (ML) methods for accelerated simulations based on a quantum mechanical (QM) description of the system. We show how recent progress in ML methods has dramatically extended the applicability range of conventional QM-based simulations, allowing to calculate industrially relevant properties with enhanced accuracy, at reduced computational cost, and for length and time scales that would have otherwise not been accessible. We illustrate the benefits of ML-accelerated atomistic simulations for industrial R&D processes by showcasing relevant applications from two very different areas, drug discovery (pharmaceuticals) and energy materials. Writing from the perspective of both a molecular and a materials modeling scientist, this review aims to provide a unified picture of the impact of ML-accelerated atomistic simulations on the pharmaceutical, chemical, and materials industries and gives an outlook on the exciting opportunities that could emerge in the future.
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Affiliation(s)
- Tobias Morawietz
- Bayer AG, Pharmaceuticals, R&D, Digital Technologies, Computational Molecular Design, 42096 Wuppertal, Germany
| | - Nongnuch Artrith
- Department of Chemical Engineering, Columbia University, New York, NY 10027 USA
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38
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Giese TJ, York DM. Variational Method for Networkwide Analysis of Relative Ligand Binding Free Energies with Loop Closure and Experimental Constraints. J Chem Theory Comput 2021; 17:1326-1336. [PMID: 33528251 PMCID: PMC8011336 DOI: 10.1021/acs.jctc.0c01219] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We describe an efficient method for the simultaneous solution of all free energies within a relative binding free-energy (RBFE) network with cycle closure and experimental/reference constraint conditions using Bennett Acceptance Ratio (BAR) and Multistate BAR (MBAR) analysis. Rather than solving the BAR or MBAR equations for each transformation independently, the simultaneous solution of all transformations are obtained by performing a constrained minimization of a global objective function. The nonlinear optimization of the objective function is subjected to affine linear constraints that couple the free energies between the network edges. The constraints are used to enforce the closure of thermodynamic cycles within the RBFE network, and to enforce an additional set of linear constraint conditions demonstrated here to be subsets of (1 or 2) experimental values. We describe details of the practical implementation of the network BAR/MBAR procedure, including use of generalized coordinates in the minimization of the free-energy objective function, propagation of bootstrap errors from those coordinates, and performance and memory optimization. In some cases it is found that use of restraints in the optimization is more practical than use of generalized coordinates for enforcing constraint conditions. The fast BARnet and MBARnet methods are used to analyze the RBFEs of six prototypical protein-ligand systems, and it is shown that enforcement of cycle closure conditions reduces the error in the predictions only modestly, and further reduction in errors can be achieved when one or two experimental RBFEs are included in the optimization procedure. These methods have been implemented into FE-ToolKit, a new free-energy analysis toolkit. The BARnet/MBARnet framework presented here opens the door to new, more efficient and robust free-energy analysis with enhanced predictive capability for drug discovery applications.
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Affiliation(s)
- Timothy J. Giese
- Laboratory for Biomolecular Simulation Research, Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087 USA
| | - Darrin M. York
- Laboratory for Biomolecular Simulation Research, Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087 USA
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39
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2,2-Dimethyl-3-[(4-methylphenyl)sulfonyl]-2,3-dihydro-1,3,2-benzoxazasilole: synthesis, properties, and structure. Russ Chem Bull 2021. [DOI: 10.1007/s11172-021-3097-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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40
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Schaller D, Pach S, Bermudez M, Wolber G. Exploiting Water Dynamics for Pharmacophore Screening. Methods Mol Biol 2021; 2266:227-238. [PMID: 33759130 DOI: 10.1007/978-1-0716-1209-5_13] [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: 06/12/2023]
Abstract
Three-dimensional pharmacophore models have been proven extremely valuable in exploring novel chemical space through virtual screening. However, traditional pharmacophore-based approaches need ligand information and rely on static snapshots of highly dynamic systems. In this chapter, we describe PyRod, a novel tool to generate three-dimensional pharmacophore models based on water traces of a molecular dynamics simulation of an apo-protein.The protocol described herein was successfully applied for the discovery of novel drug-like inhibitors of West Nile virus NS2B-NS3 protease. By using this recent example, we highlight the key steps of the generation and validation of PyRod-derived pharmacophore models and their application for virtual screening.
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Affiliation(s)
- David Schaller
- Pharmaceutical and Medicinal Chemistry, Freie Universität Berlin, Berlin, Germany
| | - Szymon Pach
- Pharmaceutical and Medicinal Chemistry, Freie Universität Berlin, Berlin, Germany
| | - Marcel Bermudez
- Pharmaceutical and Medicinal Chemistry, Freie Universität Berlin, Berlin, Germany
| | - Gerhard Wolber
- Pharmaceutical and Medicinal Chemistry, Freie Universität Berlin, Berlin, Germany.
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41
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Ferraro M, Moroni E, Ippoliti E, Rinaldi S, Sanchez-Martin C, Rasola A, Pavarino LF, Colombo G. Machine Learning of Allosteric Effects: The Analysis of Ligand-Induced Dynamics to Predict Functional Effects in TRAP1. J Phys Chem B 2020; 125:101-114. [PMID: 33369425 PMCID: PMC8016192 DOI: 10.1021/acs.jpcb.0c09742] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
Allosteric
molecules provide a powerful means to modulate protein
function. However, the effect of such ligands on distal orthosteric
sites cannot be easily described by classical docking methods. Here,
we applied machine learning (ML) approaches to expose the links between
local dynamic patterns and different degrees of allosteric inhibition
of the ATPase function in the molecular chaperone TRAP1. We focused
on 11 novel allosteric modulators with similar affinities to the target
but with inhibitory efficacy between the 26.3 and 76%. Using a set
of experimentally related local descriptors, ML enabled us to connect
the molecular dynamics (MD) accessible to ligand-bound (perturbed)
and unbound (unperturbed) systems to the degree of ATPase allosteric
inhibition. The ML analysis of the comparative perturbed ensembles
revealed a redistribution of dynamic states in the inhibitor-bound
versus inhibitor-free systems following allosteric binding. Linear
regression models were built to quantify the percentage of experimental
variance explained by the predicted inhibitor-bound TRAP1 states.
Our strategy provides a comparative MD–ML framework to infer
allosteric ligand functionality. Alleviating the time scale issues
which prevent the routine use of MD, a combination of MD and ML represents
a promising strategy to support in silico mechanistic
studies and drug design.
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Affiliation(s)
- Mariarosaria Ferraro
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta"- SCITEC, Via Mario Bianco 9, 20131 Milano, Italy
| | - Elisabetta Moroni
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta"- SCITEC, Via Mario Bianco 9, 20131 Milano, Italy
| | - Emiliano Ippoliti
- Institute for Advanced Simulation (IAS-5) and Institute of Neuroscience and Medicine (INM-9), Computational Biomedicine, Forschungszentrum Jülich, 52425 Jülich, Germany.,JARA-HPC, Forschungszentrum Jülich, D-54245 Jülich, Germany
| | - Silvia Rinaldi
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta"- SCITEC, Via Mario Bianco 9, 20131 Milano, Italy
| | - Carlos Sanchez-Martin
- Dipartimento di Scienze Biomediche, Università di Padova, viale G. Colombo 3, 35131 Padova, Italy
| | - Andrea Rasola
- Dipartimento di Scienze Biomediche, Università di Padova, viale G. Colombo 3, 35131 Padova, Italy
| | - Luca F Pavarino
- Dipartimento di Matematica "F. Casorati", Università di Pavia, Via Ferrata 5, 27100 Pavia Italy
| | - Giorgio Colombo
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta"- SCITEC, Via Mario Bianco 9, 20131 Milano, Italy.,Dipartimento di Chimica, Università di Pavia, via Taramelli 12, 27100 Pavia, Italy
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42
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Integrating molecular modelling methods to advance influenza A virus drug discovery. Drug Discov Today 2020; 26:503-510. [PMID: 33220433 DOI: 10.1016/j.drudis.2020.11.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 10/20/2020] [Accepted: 11/11/2020] [Indexed: 11/20/2022]
Abstract
Since the discovery of the anti-influenza drugs oseltamivir and zanamivir using computer-aided drug design methods, there have been significant applications of molecular modelling methodologies applied to influenza A virus drug discovery, such as molecular dynamics (MD) simulation, molecular docking, and virtual screening (VS). In this review, we provide a brief general introduction to molecular modelling in the context of drug discovery and then focus on the advances and impact of integrating these methods with specific reference to potential influenza A antiviral drug targets.
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43
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Jednačak T, Mikulandra I, Novak P. Advanced Methods for Studying Structure and Interactions of Macrolide Antibiotics. Int J Mol Sci 2020; 21:E7799. [PMID: 33096889 PMCID: PMC7589898 DOI: 10.3390/ijms21207799] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 10/09/2020] [Accepted: 10/19/2020] [Indexed: 11/17/2022] Open
Abstract
Macrolide antibiotics are macrocyclic compounds that are clinically used and prescribed for the treatment of upper and lower respiratory tract infections. They inhibit the synthesis of bacterial proteins by reversible binding to the 23S rRNA at or near the peptidyl transferase center. However, their excellent antibacterial profile was largely compromised by the emergence of bacterial resistance. Today, fighting resistance to antibiotics is one of the greatest challenges in medicinal chemistry. Considering various physicochemical properties of macrolides, understanding their structure and interactions with macromolecular targets is crucial for the design of new antibiotics efficient against resistant pathogens. The solid-state structures of some macrolide-ribosome complexes have recently been solved, throwing new light on the macrolide binding mechanisms. On the other hand, a combination of NMR spectroscopy and molecular modeling calculations can be applied to study free and bound conformations in solution. In this article, a description of advanced physicochemical methods for elucidating the structure and interactions of macrolide antibiotics in solid state and solution will be provided, and their principal advantages and drawbacks will be discussed.
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Affiliation(s)
- Tomislav Jednačak
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, HR-10000 Zagreb, Croatia;
| | | | - Predrag Novak
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, HR-10000 Zagreb, Croatia;
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44
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Bluntzer MTJ, O'Connell J, Baker TS, Michel J, Hulme AN. Designing stapled peptides to inhibit
protein‐protein
interactions: An analysis of successes in a rapidly changing field. Pept Sci (Hoboken) 2020. [DOI: 10.1002/pep2.24191] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
| | | | | | - Julien Michel
- EaStChem School of Chemistry The University of Edinburgh Edinburgh UK
| | - Alison N. Hulme
- EaStChem School of Chemistry The University of Edinburgh Edinburgh UK
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45
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Long S, Resende DISP, Palmeira A, Kijjoa A, Silva AMS, Tiritan ME, Pereira-Terra P, Freitas-Silva J, Barreiro S, Silva R, Remião F, Pinto E, Martins da Costa P, Sousa E, Pinto MMM. New marine-derived indolymethyl pyrazinoquinazoline alkaloids with promising antimicrobial profiles. RSC Adv 2020; 10:31187-31204. [PMID: 35520644 PMCID: PMC9056383 DOI: 10.1039/d0ra05319h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 08/11/2020] [Indexed: 01/03/2023] Open
Abstract
Due to the emergence of multidrug-resistant pathogenic microorganisms, the search for novel antimicrobials is urgent. Inspired by marine alkaloids, a series of indolomethyl pyrazino [1,2-b]quinazoline-3,6-diones was prepared using a one-pot microwave-assisted multicomponent polycondensation of amino acids. The compounds were evaluated for their antimicrobial activity against a panel of nine bacterial strains and five fungal strains. Compounds 26 and 27 were the most effective against Staphylococcus aureus ATCC 29213 reference strain with MIC values of 4 μg mL−1, and a methicillin-resistant Staphylococcus aureus (MRSA) isolate with MIC values of 8 μg mL−1. It was possible to infer that enantiomer (−)-26 was responsible for the antibacterial activity (MIC 4 μg mL−1) while (+)-26 had no activity. Furthermore, compound (−)-26 was able to impair S. aureus biofilm production and no significant cytotoxicity towards differentiated and non-differentiated SH-SY5Y cells was observed. Compounds 26, 28, and 29 showed a weak antifungal activity against Trichophyton rubrum clinical isolate with MIC 128 μg mL−1 and presented a synergistic effect with fluconazole. Indolomethyl pyrazino [1,2-b]quinazoline-3,6-diones were prepared using a one-pot multicomponent polycondensation of amino acids and were evaluated for their antimicrobial activity against a panel of nine bacterial strains and five fungal strains.![]()
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Affiliation(s)
- Solida Long
- LQOF - Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto Rua de Jorge Viterbo Ferreira, 228 4050-313 Porto Portugal
| | - Diana I S P Resende
- LQOF - Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto Rua de Jorge Viterbo Ferreira, 228 4050-313 Porto Portugal .,CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Terminal de Cruzeiros do Porto de Leixões Av. General Norton de Matos S/N 4450-208 Matosinhos Portugal
| | - Andreia Palmeira
- LQOF - Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto Rua de Jorge Viterbo Ferreira, 228 4050-313 Porto Portugal .,CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Terminal de Cruzeiros do Porto de Leixões Av. General Norton de Matos S/N 4450-208 Matosinhos Portugal
| | - Anake Kijjoa
- CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Terminal de Cruzeiros do Porto de Leixões Av. General Norton de Matos S/N 4450-208 Matosinhos Portugal.,ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto Rua de Jorge Viterbo Ferreira, 228 4050-313 Porto Portugal
| | - Artur M S Silva
- QOPNA - Química Orgânica, Produtos Naturais e Agroalimentares, Departamento de Química, Universidade de Aveiro 3810-193 Aveiro Portugal
| | - Maria Elizabeth Tiritan
- LQOF - Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto Rua de Jorge Viterbo Ferreira, 228 4050-313 Porto Portugal .,CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Terminal de Cruzeiros do Porto de Leixões Av. General Norton de Matos S/N 4450-208 Matosinhos Portugal.,CESPU, Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde (IINFACTS) Rua Central de Gandra, 1317 4585-116 Gandra PRD Portugal
| | - Patrícia Pereira-Terra
- CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Terminal de Cruzeiros do Porto de Leixões Av. General Norton de Matos S/N 4450-208 Matosinhos Portugal.,ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto Rua de Jorge Viterbo Ferreira, 228 4050-313 Porto Portugal
| | - Joana Freitas-Silva
- CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Terminal de Cruzeiros do Porto de Leixões Av. General Norton de Matos S/N 4450-208 Matosinhos Portugal.,ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto Rua de Jorge Viterbo Ferreira, 228 4050-313 Porto Portugal
| | - Sandra Barreiro
- UCIBIO-REQUIMTE, Laboratório de Toxicologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto Rua de Jorge Viterbo Ferreira, 228 4050-313 Porto Portugal
| | - Renata Silva
- UCIBIO-REQUIMTE, Laboratório de Toxicologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto Rua de Jorge Viterbo Ferreira, 228 4050-313 Porto Portugal
| | - Fernando Remião
- UCIBIO-REQUIMTE, Laboratório de Toxicologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto Rua de Jorge Viterbo Ferreira, 228 4050-313 Porto Portugal
| | - Eugénia Pinto
- CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Terminal de Cruzeiros do Porto de Leixões Av. General Norton de Matos S/N 4450-208 Matosinhos Portugal.,Laboratório de Microbiologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto Rua de Jorge Viterbo Ferreira, 228 4050-313 Porto Portugal
| | - Paulo Martins da Costa
- CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Terminal de Cruzeiros do Porto de Leixões Av. General Norton de Matos S/N 4450-208 Matosinhos Portugal.,ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto Rua de Jorge Viterbo Ferreira, 228 4050-313 Porto Portugal
| | - Emília Sousa
- LQOF - Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto Rua de Jorge Viterbo Ferreira, 228 4050-313 Porto Portugal .,CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Terminal de Cruzeiros do Porto de Leixões Av. General Norton de Matos S/N 4450-208 Matosinhos Portugal
| | - Madalena M M Pinto
- LQOF - Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto Rua de Jorge Viterbo Ferreira, 228 4050-313 Porto Portugal .,CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Terminal de Cruzeiros do Porto de Leixões Av. General Norton de Matos S/N 4450-208 Matosinhos Portugal
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Lans I, Anoz-Carbonell E, Palacio-Rodríguez K, Aínsa JA, Medina M, Cossio P. In silico discovery and biological validation of ligands of FAD synthase, a promising new antimicrobial target. PLoS Comput Biol 2020; 16:e1007898. [PMID: 32797038 PMCID: PMC7449411 DOI: 10.1371/journal.pcbi.1007898] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 08/26/2020] [Accepted: 07/09/2020] [Indexed: 01/06/2023] Open
Abstract
New treatments for diseases caused by antimicrobial-resistant microorganisms can be developed by identifying unexplored therapeutic targets and by designing efficient drug screening protocols. In this study, we have screened a library of compounds to find ligands for the flavin-adenine dinucleotide synthase (FADS) -a potential target for drug design against tuberculosis and pneumonia- by implementing a new and efficient virtual screening protocol. The protocol has been developed for the in silico search of ligands of unexplored therapeutic targets, for which limited information about ligands or ligand-receptor structures is available. It implements an integrative funnel-like strategy with filtering layers that increase in computational accuracy. The protocol starts with a pharmacophore-based virtual screening strategy that uses ligand-free receptor conformations from molecular dynamics (MD) simulations. Then, it performs a molecular docking stage using several docking programs and an exponential consensus ranking strategy. The last filter, samples the conformations of compounds bound to the target using MD simulations. The MD conformations are scored using several traditional scoring functions in combination with a newly-proposed score that takes into account the fluctuations of the molecule with a Morse-based potential. The protocol was optimized and validated using a compound library with known ligands of the Corynebacterium ammoniagenes FADS. Then, it was used to find new FADS ligands from a compound library of 14,000 molecules. A small set of 17 in silico filtered molecules were tested experimentally. We identified five inhibitors of the activity of the flavin adenylyl transferase module of the FADS, and some of them were able to inhibit growth of three bacterial species: C. ammoniagenes, Mycobacterium tuberculosis, and Streptococcus pneumoniae, where the last two are human pathogens. Overall, the results show that the integrative VS protocol is a cost-effective solution for the discovery of ligands of unexplored therapeutic targets.
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Affiliation(s)
- Isaias Lans
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia UdeA, Medellin, Colombia
| | - Ernesto Anoz-Carbonell
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos (Unidades Asociadas BIFI-IQFR y CBsC-CSIC), Universidad de Zaragoza, Spain
- Grupo de Genética de Micobacterias, Departamento de Microbiología, Pediatría, Radiología y Salud Pública. Facultad de Medicina, Universidad de Zaragoza, Zaragoza, Spain
| | - Karen Palacio-Rodríguez
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia UdeA, Medellin, Colombia
| | - José Antonio Aínsa
- Instituto de Biocomputación y Física de Sistemas Complejos (Unidades Asociadas BIFI-IQFR y CBsC-CSIC), Universidad de Zaragoza, Spain
- Grupo de Genética de Micobacterias, Departamento de Microbiología, Pediatría, Radiología y Salud Pública. Facultad de Medicina, Universidad de Zaragoza, Zaragoza, Spain
- CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Spain
| | - Milagros Medina
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos (Unidades Asociadas BIFI-IQFR y CBsC-CSIC), Universidad de Zaragoza, Spain
| | - Pilar Cossio
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia UdeA, Medellin, Colombia
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt, Germany
- * E-mail:
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47
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Seshan G, Kanagasabai S, Ananthasri S, Kannappan B, Suvitha A, Jaimohan SM, Kanagaraj S, Kothandan G. Insights of structure-based pharmacophore studies and inhibitor design against Gal3 receptor through molecular dynamics simulations. J Biomol Struct Dyn 2020; 39:6987-6999. [PMID: 32772816 DOI: 10.1080/07391102.2020.1804452] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Our present work studies the structure-based pharmacophore modeling and designing inhibitor against Gal3 receptor through molecular dynamics (MD) simulations extensively. Pharmacophore models play a key role in computer-aided drug discovery like in the case of virtual screening of chemical databases, de novo drug design and lead optimization. Structure-based methods for developing pharmacophore models are important, and there have been a number of studies combining such methods with the use of MD simulations to model protein's flexibility. The two potential antagonists SNAP 37889 and SNAP 398299 were docked and simulated for 250 ns and the results are analyzed and carried for the structure-based pharmacophore studies. This helped in identification of the subtype selectivity of the binding sites of the Gal3 receptor. Our work mainly focuses on identifying these binding site residues and to design more potent inhibitors compared to the previously available inhibitors through pharmacophore models. The study provides crucial insight into the binding site residues Ala2, Asp3, Ala4, Gln5, Phe24, Gln79, Ala80, Ile82, Tyr83, Trp88, His99, Ile102, Tyr103, Met106, Tyr157, Tyr161, Pro174, Trp176, Arg181, Ala183, Leu184, Asp185, Thr188, Trp248, His251, His252, Ile255, Leu256, Phe258, Trp259, Tyr270, Arg273, Leu274 and His277, which plays a significant role in the conformational changes of the receptor and helps to understand the inhibition mechanism. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Gunalan Seshan
- Biopolymer Modelling Laboratory, Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai, Tamil Nadu, India
| | - Somarathinam Kanagasabai
- Biopolymer Modelling Laboratory, Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai, Tamil Nadu, India
| | - Sailapathi Ananthasri
- Biopolymer Modelling Laboratory, Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai, Tamil Nadu, India
| | - Balaji Kannappan
- National Research Center for Dementia, Department of Life Science, Chosun University, Gwangju, South Korea
| | - A Suvitha
- Department of Physics, CMR Institute of Technology, Bangalore, Karnataka, India
| | - S M Jaimohan
- Advanced Materials Laboratory, CSIR-Central Leather Research Institute, Chennai, Tamil Nadu, India
| | - Sekar Kanagaraj
- Laboratory for Structural Biology and Biocomputing, Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, Karnataka, India
| | - Gugan Kothandan
- Biopolymer Modelling Laboratory, Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai, Tamil Nadu, India
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48
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Gulsevin A. Nicotinic receptor pharmacology in silico: Insights and challenges. Neuropharmacology 2020; 177:108257. [PMID: 32738311 DOI: 10.1016/j.neuropharm.2020.108257] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 07/16/2020] [Accepted: 07/26/2020] [Indexed: 02/07/2023]
Abstract
Nicotinic acetylcholine receptors (nAChR) are homo- or hetero-pentameric ligand-gated ion channels of the Cys-loop superfamily and play important roles in the nervous system and muscles. Studies on nAChR benefit from in silico modeling due to the lack of high-resolution structures for most receptor subtypes and challenges in experiments addressing the complex mechanism of activation involving allosteric sites. Although there is myriad of computational modeling studies on nAChR, the multitude of the methods and parameters used in these studies makes modeling nAChR a daunting task, particularly for the non-experts in the field. To address this problem, the modeling literature on Torpedo nAChR and α7 nAChR were focused on as examples of heteromeric and homomeric nAChR, and the key in silico modeling studies between the years 1995-2019 were concisely reviewed. This was followed by a critical analysis of these studies by comparing the findings with each other and with the emerging experimental and computational data on nAChR. Based on these critical analyses, suggestions were made to guide the future researchers in the field of in silico modeling of nAChR. This article is part of the special issue on 'Contemporary Advances in Nicotine Neuropharmacology'.
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Affiliation(s)
- Alican Gulsevin
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA, 37221.
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Schaller D, Wolber G. PyRod Enables Rational Homology Model‐based Virtual Screening Against MCHR1. Mol Inform 2020; 39:e2000020. [PMID: 32329245 PMCID: PMC7317519 DOI: 10.1002/minf.202000020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 04/19/2020] [Indexed: 12/29/2022]
Abstract
Several encouraging pre‐clinical results highlight the melanin‐concentrating hormone receptor 1 (MCHR1) as promising target for anti‐obesity drug development. Currently however, experimentally resolved structures of MCHR1 are not available, which complicates rational drug design campaigns. In this study, we aimed at developing accurate, homologymodel‐based 3D pharmacophores against MCHR1. We show that traditional approaches involving docking of known active small molecules are hindered by the flexibility of binding pocket residues. Instead, we derived three‐dimensional pharmacophores from molecular dynamics simulations by employing our novel open‐source software PyRod. In a retrospective evaluation, the generated 3D pharmacophores were highly predictive returning up to 35 % of active molecules and showing an early enrichment (EF1) of up to 27.6. Furthermore, PyRod pharmacophores demonstrate higher sensitivity than ligand‐based pharmacophores and deliver structural insights, which are key to rational lead optimization.
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Affiliation(s)
- David Schaller
- Pharmaceutical and Medicinal ChemistryFreie Universität Berlin Königin-Luise-Strasse 2+4 14195 Berlin Germany
| | - Gerhard Wolber
- Pharmaceutical and Medicinal ChemistryFreie Universität Berlin Königin-Luise-Strasse 2+4 14195 Berlin Germany
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50
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Ancy I, Sivanandam M, Kalaivani R, Kumaradhas P. Insights of inhibition mechanism of sifuvirtide and MT-sifuvirtide against wild and mutant HIV-1 envelope glycoprotein41: a molecular dynamics simulation and binding free energy study. MOLECULAR SIMULATION 2020. [DOI: 10.1080/08927022.2020.1716978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Iruthayaraj Ancy
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, India
| | - Magudeeswaran Sivanandam
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, India
| | - Raju Kalaivani
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, India
| | - Poomani Kumaradhas
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, India
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