1
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Yang H, Zingaro VA, Lincoff J, Tom H, Oikawa S, Oses-Prieto JA, Edmondson Q, Seiple I, Shah H, Kajimura S, Burlingame AL, Grabe M, Ruggero D. Remodelling of the translatome controls diet and its impact on tumorigenesis. Nature 2024; 633:189-197. [PMID: 39143206 DOI: 10.1038/s41586-024-07781-7] [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: 04/15/2023] [Accepted: 07/03/2024] [Indexed: 08/16/2024]
Abstract
Fasting is associated with a range of health benefits1-6. How fasting signals elicit changes in the proteome to establish metabolic programmes remains poorly understood. Here we show that hepatocytes selectively remodel the translatome while global translation is paradoxically downregulated during fasting7,8. We discover that phosphorylation of eukaryotic translation initiation factor 4E (P-eIF4E) is induced during fasting. We show that P-eIF4E is responsible for controlling the translation of genes involved in lipid catabolism and the production of ketone bodies. Inhibiting P-eIF4E impairs ketogenesis in response to fasting and a ketogenic diet. P-eIF4E regulates those messenger RNAs through a specific translation regulatory element within their 5' untranslated regions (5' UTRs). Our findings reveal a new signalling property of fatty acids, which are elevated during fasting. We found that fatty acids bind and induce AMP-activated protein kinase (AMPK) kinase activity that in turn enhances the phosphorylation of MAP kinase-interacting protein kinase (MNK), the kinase that phosphorylates eIF4E. The AMPK-MNK-eIF4E axis controls ketogenesis, revealing a new lipid-mediated kinase signalling pathway that links ketogenesis to translation control. Certain types of cancer use ketone bodies as an energy source9,10 that may rely on P-eIF4E. Our findings reveal that on a ketogenic diet, treatment with eFT508 (also known as tomivosertib; a P-eIF4E inhibitor) restrains pancreatic tumour growth. Thus, our findings unveil a new fatty acid-induced signalling pathway that activates selective translation, which underlies ketogenesis and provides a tailored diet intervention therapy for cancer.
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Affiliation(s)
- Haojun Yang
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, CA, USA
- School of Medicine and Department of Urology, UCSF, San Francisco, CA, USA
| | - Vincenzo Andrea Zingaro
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, CA, USA
- School of Medicine and Department of Urology, UCSF, San Francisco, CA, USA
| | - James Lincoff
- Department of Pharmaceutical Chemistry, UCSF, San Francisco, CA, USA
- Cardiovascular Research Institute, UCSF, San Francisco, CA, USA
| | - Harrison Tom
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, CA, USA
- School of Medicine and Department of Urology, UCSF, San Francisco, CA, USA
| | - Satoshi Oikawa
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center, Harvard Medical School and Howard Hughes Medical Institute, Boston, MA, USA
| | | | - Quinn Edmondson
- Department of Pharmaceutical Chemistry, UCSF, San Francisco, CA, USA
- Cardiovascular Research Institute, UCSF, San Francisco, CA, USA
| | - Ian Seiple
- Department of Pharmaceutical Chemistry, UCSF, San Francisco, CA, USA
- Cardiovascular Research Institute, UCSF, San Francisco, CA, USA
| | - Hardik Shah
- Metabolomics Platform, Comprehensive Cancer Center, The University of Chicago, Chicago, IL, USA
| | - Shingo Kajimura
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center, Harvard Medical School and Howard Hughes Medical Institute, Boston, MA, USA
| | - Alma L Burlingame
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, UCSF, San Francisco, CA, USA
| | - Michael Grabe
- Department of Pharmaceutical Chemistry, UCSF, San Francisco, CA, USA
- Cardiovascular Research Institute, UCSF, San Francisco, CA, USA
| | - Davide Ruggero
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, CA, USA.
- School of Medicine and Department of Urology, UCSF, San Francisco, CA, USA.
- Department of Cellular and Molecular Pharmacology, UCSF, San Francisco, CA, USA.
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2
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Lundborg M, Wennberg C, Lindahl E, Norlén L. Simulating the Skin Permeation Process of Ionizable Molecules. J Chem Inf Model 2024; 64:5295-5302. [PMID: 38917349 PMCID: PMC11234375 DOI: 10.1021/acs.jcim.4c00722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2024]
Abstract
It is commonly assumed that ionizable molecules, such as drugs, permeate through the skin barrier in their neutral form. By using molecular dynamics simulations of the charged and neutral states separately, we can study the dynamic protonation behavior during the permeation process. We have studied three weak acids and three weak bases and conclude that the acids are ionized to a larger extent than the bases, when passing through the headgroup region of the lipid barrier structure, at pH values close to their pKa. It can also be observed that even if these dynamic protonation simulations are informative, in the cases studied herein they are not necessary for the calculation of permeability coefficients. It is sufficient to base the calculations only on the neutral form, as is commonly done.
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Affiliation(s)
- Magnus Lundborg
- SciLifeLab, ERCO Pharma AB, 171 65 Solna, Sweden
- Department of Applied Physics, SciLifeLab, KTH Royal Institute of Technology, 106 91 Stockholm, Sweden
| | - Christian Wennberg
- SciLifeLab, ERCO Pharma AB, 171 65 Solna, Sweden
- UC AB, 111 64 Stockholm, Sweden
| | - Erik Lindahl
- Department of Biophysics and Biochemistry, SciLifeLab, Stockholm University, 106 91 Stockholm, Sweden
- Department of Applied Physics, Swedish e-Science Research Center, KTH Royal Institute of Technology, 106 91 Stockholm, Sweden
| | - Lars Norlén
- Department of Cell and Molecular Biology (CMB), Karolinska Institutet, 171 77 Solna, Sweden
- Dermatology Clinic, Karolinska University Hospital, 171 77 Solna, Sweden
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3
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Sun M, Zhang Y, Zhang XQ, Zhang Y, Wang XD, Li JT, Si TM, Su YA. Dopamine D1 receptor in medial prefrontal cortex mediates the effects of TAAR1 activation on chronic stress-induced cognitive and social deficits. Neuropsychopharmacology 2024; 49:1341-1351. [PMID: 38658737 PMCID: PMC11224251 DOI: 10.1038/s41386-024-01866-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 04/06/2024] [Accepted: 04/10/2024] [Indexed: 04/26/2024]
Abstract
Trace amine-associated receptor 1 (TAAR1) is an intracellular expressed G-protein-coupled receptor that is widely expressed in major dopaminergic areas and plays a crucial role in modulation of central dopaminergic neurotransmission and function. Pharmacological studies have clarified the roles of dopamine D1 receptor (D1R) in the medial prefrontal cortex (mPFC) in cognitive function and social behaviors, and chronic stress can inhibit D1R expression due to its susceptibility. Recently, we identified TAAR1 in the mPFC as a potential target for treating chronic stress-induced cognitive and social dysfunction, but whether D1R is involved in mediating the effects of TAAR1 agonist remains unclear. Combined genomics and transcriptomic studies revealed downregulation of D1R in the mPFC of TAAR1-/- mice. Molecular dynamics simulation showed that hydrogen bond, salt bridge, and Pi-Pi stacking interactions were formed between TAAR1 and D1R indicating a stable TAAR1-D1R complex structure. Using pharmacological interventions, we found that D1R antagonist disrupted therapeutic effect of TAAR1 partial agonist RO5263397 on stress-related cognitive and social dysfunction. Knockout TAAR1 in D1-type dopamine receptor-expressing neurons reproduced adverse effects of chronic stress, and TAAR1 conditional knockout in the mPFC led to similar deficits, along with downregulation of D1R expression, all of these effects were ameliorated by viral overexpression of D1R in the mPFC, suggesting the functional interaction between TAAR1 and D1R. Collectively, our data elucidate the possible molecular mechanism that D1R in the mPFC mediates the effects of TAAR1 activation on chronic stress-induced cognitive and social deficits.
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Affiliation(s)
- Meng Sun
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, China
| | - Yue Zhang
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, China
| | - Xian-Qiang Zhang
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, China
| | - Yanan Zhang
- Research Triangle Institute, Research Triangle Park, NC, 27709, USA
| | - Xiao-Dong Wang
- Department of Neurobiology, Key Laboratory of Medical Neurobiology of Ministry of Health of China, Zhejiang Province Key Laboratory of Neurobiology, Zhejiang University School of Medicine, 310058, Hangzhou, China
| | - Ji-Tao Li
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, China
| | - Tian-Mei Si
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, China.
| | - Yun-Ai Su
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, China.
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4
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Fedurek P, Asiimwe C, Rice GK, Akankwasa WJ, Reynolds V, Hobaiter C, Kityo R, Muhanguzi G, Zuberbühler K, Crockford C, Cer RZ, Bennett AJ, Rothman JM, Bishop-Lilly KA, Goldberg TL. Selective deforestation and exposure of African wildlife to bat-borne viruses. Commun Biol 2024; 7:470. [PMID: 38649441 PMCID: PMC11035629 DOI: 10.1038/s42003-024-06139-z] [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: 05/23/2023] [Accepted: 04/02/2024] [Indexed: 04/25/2024] Open
Abstract
Proposed mechanisms of zoonotic virus spillover often posit that wildlife transmission and amplification precede human outbreaks. Between 2006 and 2012, the palm Raphia farinifera, a rich source of dietary minerals for wildlife, was nearly extirpated from Budongo Forest, Uganda. Since then, chimpanzees, black-and-white colobus, and red duiker were observed feeding on bat guano, a behavior not previously observed. Here we show that guano consumption may be a response to dietary mineral scarcity and may expose wildlife to bat-borne viruses. Videos from 2017-2019 recorded 839 instances of guano consumption by the aforementioned species. Nutritional analysis of the guano revealed high concentrations of sodium, potassium, magnesium and phosphorus. Metagenomic analyses of the guano identified 27 eukaryotic viruses, including a novel betacoronavirus. Our findings illustrate how "upstream" drivers such as socioeconomics and resource extraction can initiate elaborate chains of causation, ultimately increasing virus spillover risk.
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Affiliation(s)
- Pawel Fedurek
- Division of Psychology, Faculty of Natural Sciences, University of Stirling, Stirling, FK9 4LA, UK
- Budongo Conservation Field Station, PO Box 362, Masindi, Uganda
| | | | - Gregory K Rice
- Biological Defense Research Directorate, Naval Medical Research Command, Fort Detrick, MD, 21702, USA
- Leidos, 1750 Presidents St, Reston, VA, 20190, USA
| | | | - Vernon Reynolds
- Budongo Conservation Field Station, PO Box 362, Masindi, Uganda
- School of Anthropology, University of Oxford, 51/53 Banbury Road, Oxford, OX2 6PE, UK
| | - Catherine Hobaiter
- Budongo Conservation Field Station, PO Box 362, Masindi, Uganda
- School of Psychology and Neuroscience, University of St Andrews; St Mary's Quad, South Street, St Andrews, KY16 9JP, UK
| | - Robert Kityo
- Department of Zoology, Entomology & Fisheries Sciences, Makerere University, PO Box 7062, Kampala, Uganda
| | | | - Klaus Zuberbühler
- Budongo Conservation Field Station, PO Box 362, Masindi, Uganda
- School of Psychology and Neuroscience, University of St Andrews; St Mary's Quad, South Street, St Andrews, KY16 9JP, UK
- Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, CH-2000, Neuchâtel, Switzerland
| | - Catherine Crockford
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
- Institut des Sciences Cognitives, 67 Bd Pinel, 69500, Bron, France
| | - Regina Z Cer
- Biological Defense Research Directorate, Naval Medical Research Command, Fort Detrick, MD, 21702, USA
| | - Andrew J Bennett
- Biological Defense Research Directorate, Naval Medical Research Command, Fort Detrick, MD, 21702, USA
- Leidos, 1750 Presidents St, Reston, VA, 20190, USA
| | - Jessica M Rothman
- Department of Anthropology, Hunter College of the City University of New York, 695 Park Avenue, New York, NY, 10065, USA
| | - Kimberly A Bishop-Lilly
- Biological Defense Research Directorate, Naval Medical Research Command, Fort Detrick, MD, 21702, USA
| | - Tony L Goldberg
- School of Veterinary Medicine, Department of Pathobiological Sciences, University of Wisconsin-Madison, 1656 Linden Drive, Madison, WI, USA.
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5
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Verma AK, Sharma BB. Experimental and Theoretical Insights into Interfacial Properties of 2D Materials for Selective Water Transport Membranes: A Critical Review. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:7812-7834. [PMID: 38587122 DOI: 10.1021/acs.langmuir.4c00061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Interfacial properties, such as wettability and friction, play critical roles in nanofluidics and desalination. Understanding the interfacial properties of two-dimensional (2D) materials is crucial in these applications due to the close interaction between liquids and the solid surface. The most important interfacial properties of a solid surface include the water contact angle, which quantifies the extent of interactions between the surface and water, and the water slip length, which determines how much faster water can flow on the surface beyond the predictions of continuum fluid mechanics. This Review seeks to elucidate the mechanism that governs the interfacial properties of diverse 2D materials, including transition metal dichalcogenides (e.g., MoS2), graphene, and hexagonal boron nitride (hBN). Our work consolidates existing experimental and computational insights into 2D material synthesis and modeling and explores their interfacial properties for desalination. We investigated the capabilities of density functional theory and molecular dynamics simulations in analyzing the interfacial properties of 2D materials. Specifically, we highlight how MD simulations have revolutionized our understanding of these properties, paving the way for their effective application in desalination. This Review of the synthesis and interfacial properties of 2D materials unlocks opportunities for further advancement and optimization in desalination.
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Affiliation(s)
- Ashutosh Kumar Verma
- School of Chemical Engineering, Oklahoma State University, Stillwater, Oklahoma 74078, United States
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6
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Abdel-Naim AB, Kumar P, Bazuhair MA, Rizg WY, Niyazi HA, Alkuwaity K, Niyazi HA, Alharthy SA, Harakeh S, Haque S, Prakash A, Kumar V. Computational insights into dynamics and conformational stability of N-acetylmannosamine kinase mutations. J Biomol Struct Dyn 2024:1-11. [PMID: 38502682 DOI: 10.1080/07391102.2024.2323702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 02/21/2024] [Indexed: 03/21/2024]
Abstract
The activity of UDP-GlcNAc 2-epimerase/ManNAc kinase (GNE) is essential for the biosynthesis of sialic acid, which is involved in cellular processes in health and diseases. GNE contains an N-terminal epimerase domain and a C-terminal kinase domain (N-acetylmannosamine kinase, MNK). Mutations of the GNE protein led to hypoactivity of the enzyme and cause sialurea or autosomal recessive inclusion body myopathy/Nonaka myopathy. Here, we used all-atom molecular dynamics (MD) simulations to comprehend the folding, dynamics and conformational stability of MNK variants, including the wild type (WT) and three mutants (H677R, V696M and H677R/V696M). The deleterious and destabilizing nature of MNK mutants were predicted using different prediction tools. Results predicted that mutations modulate the stability, flexibility and function of MNK. The effect of mutations on the conformational stability and dynamics of MNK was next studied through the free-energy landscape (FEL), hydrogen-bonds and secondary structure changes. The FEL results show that the mutations interfere with various conformational transitions in both WT and mutants, exposing the structural underpinnings of protein destabilization and unfolding brought on by mutation. We discover that, when compared to the other two mutations, V696M and H677R/V696M, H677R has the most harmful effects. These findings have a strong correlation with published experimental studies that demonstrate how these mutations disrupt MNK activity. Hence, this computational study describes the structural details to unravel the mutant effects at the atomistic resolution and has implications for understanding the GNE's physiological and pathological role.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ashraf B Abdel-Naim
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
- Mohamed Saeed Tamer Chair for Pharmaceutical Industries, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
- Center of Excellence for Drug Research and Pharmaceutical Industries, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Pawan Kumar
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Mohammed A Bazuhair
- Center of Excellence for Drug Research and Pharmaceutical Industries, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Clinical Pharmacology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Waleed Y Rizg
- Mohamed Saeed Tamer Chair for Pharmaceutical Industries, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
- Center of Excellence for Drug Research and Pharmaceutical Industries, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Pharmaceutics, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hatoon A Niyazi
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Khalil Alkuwaity
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hanouf A Niyazi
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Saif A Alharthy
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Toxicology and Forensic Sciences Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Steve Harakeh
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Yousef Abdul Latif Jameel Scientific Chair of Prophetic Medicine Application, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Health Sciences, Jazan University, Jazan, Saudi Arabia
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, Lebanon
- Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates
| | - Amresh Prakash
- Amity Institute of Integrative Sciences and Health, Amity University Haryana, Gurgaon, India
| | - Vijay Kumar
- Amity Institute of Neuropsychology & Neurosciences, Amity University, Noida, India
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7
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Zhuo X, Foderà V, Larsson P, Schaal Z, Bergström CAS, Löbmann K, Kabedev A. Analysis of stabilization mechanisms in β-lactoglobulin-based amorphous solid dispersions by experimental and computational approaches. Eur J Pharm Sci 2024; 192:106639. [PMID: 37967658 DOI: 10.1016/j.ejps.2023.106639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 11/09/2023] [Accepted: 11/11/2023] [Indexed: 11/17/2023]
Abstract
Our previous work shows that β-lactoglobulin-stabilized amorphous solid dispersion (ASD) loaded with 70 % indomethacin remains stable for more than 12 months. The stability is probably due to hydrogen bond networks spread throughout the ASD, facilitated by the indomethacin which has both hydrogen donors and acceptors. To investigate the stabilization mechanisms further, here we tested five other drug molecules, including two without any hydrogen bond donors. A combination of experimental techniques (differential scanning calorimetry, X-ray power diffraction) and molecular dynamics simulations was used to find the maximum drug loadings for ASDs with furosemide, griseofulvin, ibuprofen, ketoconazole and rifaximin. This approach revealed the underlying stabilization factors and the capacity of computer simulations to predict ASD stability. We searched the ASD models for crystalline patterns, and analyzed diffusivity of the drug molecules and hydrogen bond formation. ASDs loaded with rifaximin and ketoconazole remained stable for at least 12 months, even at 90 % drug loading, whereas stable drug loadings for furosemide, griseofulvin and ibuprofen were at a maximum of 70, 50 and 40 %, respectively. Steric confinement and hydrogen bonding to the proteins were the most important stabilization mechanisms at low drug loadings (≤ 40 %). Inter-drug hydrogen bond networks (including those with induced donors), ionic interactions, and a high Tg of the drug molecule were additional factors stabilizing the ASDs at drug loading greater than 40 %.
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Affiliation(s)
- Xuezhi Zhuo
- Department of Pharmacy, University of Copenhagen, Copenhagen 2100, Denmark
| | - Vito Foderà
- Department of Pharmacy, University of Copenhagen, Copenhagen 2100, Denmark
| | - Per Larsson
- Department of Pharmacy, Uppsala University, Uppsala 75123, Sweden
| | - Zarah Schaal
- Department of Pharmacy, University of Copenhagen, Copenhagen 2100, Denmark
| | | | - Korbinian Löbmann
- Department of Pharmacy, University of Copenhagen, Copenhagen 2100, Denmark; Zerion Pharma A/S, Birkerød 3460, Denmark
| | - Aleksei Kabedev
- Department of Pharmacy, Uppsala University, Uppsala 75123, Sweden.
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8
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Alamri SH, Haque S, Alghamdi BS, Tayeb HO, Azhari S, Farsi RM, Elmokadem A, Alamri TA, Harakeh S, Prakash A, Kumar V. Comprehensive mapping of mutations in TDP-43 and α-Synuclein that affect stability and binding. J Biomol Struct Dyn 2023:1-13. [PMID: 38126188 DOI: 10.1080/07391102.2023.2293258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 11/11/2023] [Indexed: 12/23/2023]
Abstract
Abnormal aggregation and amyloid inclusions of TAR DNA-binding protein 43 (TDP-43) and α-Synuclein (α-Syn) are frequently co-observed in amyotrophic lateral sclerosis, Parkinson's disease, and Alzheimer's disease. Several reports showed TDP-43 C-terminal domain (CTD) and α-Syn interact with each other and the aggregates of these two proteins colocalized together in different cellular and animal models. Molecular dynamics simulation was conducted to elucidate the stability of the TDP-43 and Syn complex structure. The interfacial mutations in protein complexes changes the stability and binding affinity of the protein that may cause diseases. Here, we have utilized the computational saturation mutagenesis approach including structure-based stability and binding energy calculations to compute the systemic effects of missense mutations of TDP-43 CTD and α-Syn on protein stability and binding affinity. Most of the interfacial mutations of CTD and α-Syn were found to destabilize the protein and reduced the protein binding affinity. The results thus shed light on the functional consequences of missense mutations observed in TDP-43 associated proteinopathies and may provide the mechanisms of co-morbidities involving these two proteins.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sultan H Alamri
- Department of Family Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, Lebanon
- Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates
| | - Badra S Alghamdi
- Department of Physiology, Neuroscience Unit, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Pre-Clinical Research Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Haythum O Tayeb
- The Mind and Brain Studies Initiative, Neuroscience Research Unit, Department of Neurology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Shereen Azhari
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Reem M Farsi
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Abear Elmokadem
- Department of Hematology/Pediatric Oncology, King Abdulaziz University Hospital, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Turki A Alamri
- Family and Community Medicine Department, Faculty of Medicine in Rabigh, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Steve Harakeh
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Jeddah, Saudi Arabia
- Yousef Abdul Latif Jameel Scientific Chair of Prophetic Medicine Application, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Amresh Prakash
- Amity Institute of Integrative Sciences and Health (AIISH), Amity University Haryana, Gurgaon, India
| | - Vijay Kumar
- Amity Institute of Neuropsychology & Neurosciences, Amity University, Noida, India
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9
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Kabedev A, Bergström CAS, Larsson P. Molecular dynamics study on micelle-small molecule interactions: developing a strategy for an extensive comparison. J Comput Aided Mol Des 2023; 38:5. [PMID: 38103089 PMCID: PMC10725378 DOI: 10.1007/s10822-023-00541-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 10/31/2023] [Indexed: 12/17/2023]
Abstract
Theoretical predictions of the solubilizing capacity of micelles and vesicles present in intestinal fluid are important for the development of new delivery techniques and bioavailability improvement. A balance between accuracy and computational cost is a key factor for an extensive study of numerous compounds in diverse environments. In this study, we aimed to determine an optimal molecular dynamics (MD) protocol to evaluate small-molecule interactions with micelles composed of bile salts and phospholipids. MD simulations were used to produce free energy profiles for three drug molecules (danazol, probucol, and prednisolone) and one surfactant molecule (sodium caprate) as a function of the distance from the colloid center of mass. To address the challenges associated with such tasks, we compared different simulation setups, including freely assembled colloids versus pre-organized spherical micelles, full free energy profiles versus only a few points of interest, and a coarse-grained model versus an all-atom model. Our findings demonstrate that combining these techniques is advantageous for achieving optimal performance and accuracy when evaluating the solubilization capacity of micelles. All-atom (AA) and coarse-grained (CG) umbrella sampling (US) simulations and point-wise free energy (FE) calculations were compared to their efficiency to computationally analyze the solubilization of active pharmaceutical ingredients in intestinal fluid colloids.
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Affiliation(s)
| | - Christel A S Bergström
- Department of Pharmacy, Uppsala University, Uppsala, Sweden
- Swedish Drug Delivery Center, Uppsala University, Uppsala, Sweden
| | - Per Larsson
- Department of Pharmacy, Uppsala University, Uppsala, Sweden.
- Swedish Drug Delivery Center, Uppsala University, Uppsala, Sweden.
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10
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Kim H, Fábián B, Hummer G. Neighbor List Artifacts in Molecular Dynamics Simulations. J Chem Theory Comput 2023; 19:8919-8929. [PMID: 38035387 PMCID: PMC10720336 DOI: 10.1021/acs.jctc.3c00777] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 10/31/2023] [Accepted: 11/01/2023] [Indexed: 12/02/2023]
Abstract
Molecular dynamics (MD) simulations are widely used in biophysical research. To aid nonexpert users, most simulation packages provide default values for key input parameters. In MD simulations using the GROMACS package with default parameters, we found large membranes to deform under the action of a semi-isotropically coupled barostat. As the primary cause, we identified overly short outer cutoffs and infrequent neighbor list updates that resulted in missed nonbonded interactions. Small but systematic imbalances in the apparent pressure tensor then induce unphysical asymmetric box deformations that crumple the membrane. We also observed rapid oscillations in averages of the instantaneous pressure tensor components and traced these to the use of a dual pair list with dynamic pruning. We confirmed that similar effects are present in MD simulations of neat water in atomistic and coarse-grained representations. Whereas the slight pressure imbalances likely have minimal impact in most current atomistic MD simulations, we expect their impact to grow in studies of ever-larger systems with coarse-grained representation, in particular, in combination with anisotropic pressure coupling. We present measures to diagnose problems with missed interactions and guidelines for practitioners to avoid them, including estimates for appropriate values for the outer cutoff rl and the number of time steps nstlist between neighbor list updates.
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Affiliation(s)
- Hyuntae Kim
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany
- International
Max Planck Research School on Cellular Biophysics, Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany
| | - Balázs Fábián
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany
| | - Gerhard Hummer
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany
- Institute
of Biophysics, Goethe University Frankfurt, Max-von-Laue-Straße 1, 60438 Frankfurt am Main, Germany
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11
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Haque S, Kumar P, Mathkor DM, Bantun F, Jalal NA, Mufti AH, Prakash A, Kumar V. In silico evaluation of the inhibitory potential of nucleocapsid inhibitors of SARS-CoV-2: a binding and energetic perspective. J Biomol Struct Dyn 2023; 41:9797-9807. [PMID: 36379684 DOI: 10.1080/07391102.2022.2146752] [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: 08/17/2022] [Accepted: 11/07/2022] [Indexed: 11/17/2022]
Abstract
The COVID-19 outbreak brought on by the SARS-CoV-2 virus continued to infect a sizable population worldwide. The SARS-CoV-2 nucleocapsid (N) protein is the most conserved RNA-binding structural protein and is a desirable target because of its involvement in viral transcription and replication. Based on this aspect, this study focused to repurpose antiviral compounds approved or in development for treating COVID-19. The inhibitors chosen are either FDA-approved or are currently being studied in clinical trials against COVID-19. Initially, they were designed to target stress granules and other RNA biology. We have utilized structure-based molecular docking and all-atom molecular dynamics (MD) simulation approach to investigate in detail the binding energy and binding modes of the different anti-N inhibitors to N protein. The result showed that five drugs including Silmitasterib, Ninetanidinb, Ternatin, Luteolin, Fedratinib, PJ34, and Zotatafin were found interacting with RNA binding sites as well as to predicted protein interface with higher binding energy. Overall, drug binding increases the stability of the complex with maximum stability found in the order, Silmitasertib > PJ34 > Zotatatafin. In addition, the frustration changes due to drug binding brings a decrease in local frustration and this decrease is mainly observed in α-helix, β3, β5, and β6 strands and are important for drug binding. Our in-silico data suggest that an effective interaction occurs for some of the tested drugs and prompt their further validation to reduce the rapid outspreading of SARS-CoV-2.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Pawan Kumar
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Darin Mansor Mathkor
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Farkad Bantun
- Department of Microbiology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Naif A Jalal
- Department of Microbiology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Ahmad Hasan Mufti
- Medical Genetics Department, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Amresh Prakash
- Amity Institute of Integrative Sciences and Health, Amity University Haryana, Gurgaon, India
| | - Vijay Kumar
- Amity Institute of Neuropsychology & Neurosciences, Amity University, Noida, Uttar Pradesh, India
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12
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Goscinski A, Principe VP, Fraux G, Kliavinek S, Helfrecht BA, Loche P, Ceriotti M, Cersonsky RK. scikit-matter : A Suite of Generalisable Machine Learning Methods Born out of Chemistry and Materials Science. OPEN RESEARCH EUROPE 2023; 3:81. [PMID: 38234865 PMCID: PMC10792272 DOI: 10.12688/openreseurope.15789.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 09/01/2023] [Indexed: 08/11/2024]
Abstract
Easy-to-use libraries such as scikit-learn have accelerated the adoption and application of machine learning (ML) workflows and data-driven methods. While many of the algorithms implemented in these libraries originated in specific scientific fields, they have gained in popularity in part because of their generalisability across multiple domains. Over the past two decades, researchers in the chemical and materials science community have put forward general-purpose machine learning methods. The deployment of these methods into workflows of other domains, however, is often burdensome due to the entanglement with domainspecific functionalities. We present the python library scikit-matter that targets domain-agnostic implementations of methods developed in the computational chemical and materials science community, following the scikit-learn API and coding guidelines to promote usability and interoperability with existing workflows.
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Affiliation(s)
- Alexander Goscinski
- Laboratory of Computational Science and Modeling (COSMO), Institute of Materials, Ecole Polytechnique Federale de Lausanne, Lausanne, Vaud, 1015, Switzerland
| | - Victor Paul Principe
- Laboratory of Computational Science and Modeling (COSMO), Institute of Materials, Ecole Polytechnique Federale de Lausanne, Lausanne, Vaud, 1015, Switzerland
| | - Guillaume Fraux
- Laboratory of Computational Science and Modeling (COSMO), Institute of Materials, Ecole Polytechnique Federale de Lausanne, Lausanne, Vaud, 1015, Switzerland
| | - Sergei Kliavinek
- Laboratory of Computational Science and Modeling (COSMO), Institute of Materials, Ecole Polytechnique Federale de Lausanne, Lausanne, Vaud, 1015, Switzerland
| | - Benjamin Aaron Helfrecht
- Laboratory of Computational Science and Modeling (COSMO), Institute of Materials, Ecole Polytechnique Federale de Lausanne, Lausanne, Vaud, 1015, Switzerland
- Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Philip Loche
- Laboratory of Computational Science and Modeling (COSMO), Institute of Materials, Ecole Polytechnique Federale de Lausanne, Lausanne, Vaud, 1015, Switzerland
| | - Michele Ceriotti
- Laboratory of Computational Science and Modeling (COSMO), Institute of Materials, Ecole Polytechnique Federale de Lausanne, Lausanne, Vaud, 1015, Switzerland
| | - Rose Kathleen Cersonsky
- Laboratory of Computational Science and Modeling (COSMO), Institute of Materials, Ecole Polytechnique Federale de Lausanne, Lausanne, Vaud, 1015, Switzerland
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
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13
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Wennberg C, Lundborg M, Lindahl E, Norlén L. Understanding Drug Skin Permeation Enhancers Using Molecular Dynamics Simulations. J Chem Inf Model 2023; 63:4900-4911. [PMID: 37462219 PMCID: PMC10428223 DOI: 10.1021/acs.jcim.3c00625] [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: 04/24/2023] [Indexed: 08/15/2023]
Abstract
Our skin constitutes an effective permeability barrier that protects the body from exogenous substances but concomitantly severely limits the number of pharmaceutical drugs that can be delivered transdermally. In topical formulation design, chemical permeation enhancers (PEs) are used to increase drug skin permeability. In vitro skin permeability experiments can measure net effects of PEs on transdermal drug transport, but they cannot explain the molecular mechanisms of interactions between drugs, permeation enhancers, and skin structure, which limits the possibility to rationally design better new drug formulations. Here we investigate the effect of the PEs water, lauric acid, geraniol, stearic acid, thymol, ethanol, oleic acid, and eucalyptol on the transdermal transport of metronidazole, caffeine, and naproxen. We use atomistic molecular dynamics (MD) simulations in combination with developed molecular models to calculate the free energy difference between 11 PE-containing formulations and the skin's barrier structure. We then utilize the results to calculate the final concentration of PEs in skin. We obtain an RMSE of 0.58 log units for calculated partition coefficients from water into the barrier structure. We then use the modified PE-containing barrier structure to calculate the PEs' permeability enhancement ratios (ERs) on transdermal metronidazole, caffeine, and naproxen transport and compare with the results obtained from in vitro experiments. We show that MD simulations are able to reproduce rankings based on ERs. However, strict quantitative correlation with experimental data needs further refinement, which is complicated by significant deviations between different measurements. Finally, we propose a model for how to use calculations of the potential of mean force of drugs across the skin's barrier structure in a topical formulation design.
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Affiliation(s)
| | - Magnus Lundborg
- Science
for Life Laboratory, ERCO Pharma AB, 171 65 Solna, Sweden
| | - Erik Lindahl
- Department
of Biophysics and Biochemistry, Stockholm
University, 106 91 Stockholm, Sweden
- Department
of Applied Physics, Swedish e-Science Research Center, KTH Royal Institute of Technology, 106 91 Stockholm, Sweden
| | - Lars Norlén
- Department
of Cell and Molecular Biology (CMB), Karolinska
Institutet, 171 77 Solna, Sweden
- Dermatology
Clinic. Karolinska University Hospital, 171 77 Solna, Sweden
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14
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Crawford B, Timalsina U, Quach CD, Craven NC, Gilmer JB, McCabe C, Cummings PT, Potoff JJ. MoSDeF-GOMC: Python Software for the Creation of Scientific Workflows for the Monte Carlo Simulation Engine GOMC. J Chem Inf Model 2023; 63:1218-1228. [PMID: 36791286 DOI: 10.1021/acs.jcim.2c01498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
MoSDeF-GOMC is a python interface for the Monte Carlo software GOMC to the Molecular Simulation Design Framework (MoSDeF) ecosystem. MoSDeF-GOMC automates the process of generating initial coordinates, assigning force field parameters, and writing coordinate (PDB), connectivity (PSF), force field parameter, and simulation control files. The software lowers entry barriers for novice users while allowing advanced users to create complex workflows that encapsulate simulation setup, execution, and data analysis in a single script. All relevant simulation parameters are encoded within the workflow, ensuring reproducible simulations. MoSDeF-GOMC's capabilities are illustrated through a number of examples, including prediction of the adsorption isotherm for CO2 in IRMOF-1, free energies of hydration for neon and radon over a broad temperature range, and the vapor-liquid coexistence curve of a four-component surrogate for the jet fuel S-8. The MoSDeF-GOMC software is available on GitHub at https://github.com/GOMC-WSU/MoSDeF-GOMC.
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Affiliation(s)
- Brad Crawford
- Department of Chemical Engineering, Wayne State University, Detroit, Michigan 48202-4050, United States
| | - Umesh Timalsina
- Institute for Software Integrated Systems (ISIS), Vanderbilt University, Nashville, Tennessee 37212, United States
| | - Co D Quach
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37235-1604, United States.,Multiscale Modeling and Simulation (MuMS) Center, Vanderbilt University, Nashville, Tennessee 37212, United States
| | - Nicholas C Craven
- Multiscale Modeling and Simulation (MuMS) Center, Vanderbilt University, Nashville, Tennessee 37212, United States.,Interdisciplinary Material Science Program, Vanderbilt University, Nashville, Tennessee 37235-0106, United States
| | - Justin B Gilmer
- Multiscale Modeling and Simulation (MuMS) Center, Vanderbilt University, Nashville, Tennessee 37212, United States.,Interdisciplinary Material Science Program, Vanderbilt University, Nashville, Tennessee 37235-0106, United States
| | - Clare McCabe
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37235-1604, United States.,Multiscale Modeling and Simulation (MuMS) Center, Vanderbilt University, Nashville, Tennessee 37212, United States
| | - Peter T Cummings
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37235-1604, United States.,Multiscale Modeling and Simulation (MuMS) Center, Vanderbilt University, Nashville, Tennessee 37212, United States
| | - Jeffrey J Potoff
- Department of Chemical Engineering, Wayne State University, Detroit, Michigan 48202-4050, United States
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15
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Costa RKM, Souza LMP, Silva RS, Souza FR, Pimentel AS. The reconciliation between the experimental and calculated octanol-water partition coefficient of 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine using atomistic molecular dynamics: an open question. J Biomol Struct Dyn 2023; 41:11510-11517. [PMID: 36715129 DOI: 10.1080/07391102.2023.2173298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 12/26/2022] [Indexed: 01/31/2023]
Abstract
The octanol-water partition coefficient of 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine (DPPC) was investigated using atomistic molecular dynamics simulations via thermodynamic integration and multistate Bennett acceptance ratio methods. The GAFF and CHARMM36 force fields were used with six water models widely used in molecular dynamics simulations. The OPC4 water model provided the best agreement with the experimental octanol-water partition coefficient of DPPC using the two force fields. However, there is still plenty of room for improvement in water models with correct estimation of surface tension that uses better and suitable non-bonded interaction parameters between water-water and water-DPPC. The Gibbs free energy of transferring DPPC from octanol to water phase was calculated to be 19.8 ± 0.3 and 20.2 ± 0.3 kcal mol-1, giving a partition coefficient of 14.5 ± 0.4 and 14.8 ± 0.3 for the GAFF and CHARMM36 force fields, respectively. This study reinforces the importance of developing new water models that reproduce experimental surface tensions to reconcile the water-water and water-DPPC non-bonded interactions and the existing discrepancy between experimental measurements of amphiphilic molecules that are important in many areas of scientific applications and industry such as biophysics, surfactant, colloids, membranes, medicine, nanotechnology, and food and pharmaceutical industries, and so on. It raises two important open questions: Is the experimental octanol-water partition coefficient of DPPC reliable? Or is its calculation accurate using the OPC4 water model? With respect to the experimental measurements, there may be non-treated aspects such as the formation of aggregates in aqueous phase and limit of detection of the applied method. And, in the calculation, some effects are not possible to be considered in a correct way or viable time such as calculating quantum effects, sampling all conformations, considering phase transitions, and correctly evaluating the intermolecular forces to estimate an accurate surface tension.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | - Rudielson Santos Silva
- Departamento de Química, Pontifícia Universidade Católica do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Felipe Rodrigues Souza
- Departamento de Química, Pontifícia Universidade Católica do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - André Silva Pimentel
- Departamento de Química, Pontifícia Universidade Católica do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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16
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Ganguly A, Tsai HC, Fernández-Pendás M, Lee TS, Giese TJ, York DM. AMBER Drug Discovery Boost Tools: Automated Workflow for Production Free-Energy Simulation Setup and Analysis (ProFESSA). J Chem Inf Model 2022; 62:6069-6083. [PMID: 36450130 PMCID: PMC9881431 DOI: 10.1021/acs.jcim.2c00879] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
We report an automated workflow for production free-energy simulation setup and analysis (ProFESSA) using the GPU-accelerated AMBER free-energy engine with enhanced sampling features and analysis tools, part of the AMBER Drug Discovery Boost package that has been integrated into the AMBER22 release. The workflow establishes a flexible, end-to-end pipeline for performing alchemical free-energy simulations that brings to bear technologies, including new enhanced sampling features and analysis tools, to practical drug discovery problems. ProFESSA provides the user with top-level control of large sets of free-energy calculations and offers access to the following key functionalities: (1) automated setup of file infrastructure; (2) enhanced conformational and alchemical sampling with the ACES method; and (3) network-wide free-energy analysis with the optional imposition of cycle closure and experimental constraints. The workflow is applied to perform absolute and relative solvation free-energy and relative ligand-protein binding free-energy calculations using different atom-mapping procedures. Results demonstrate that the workflow is internally consistent and highly robust. Further, the application of a new network-wide Lagrange multiplier constraint analysis that imposes key experimental constraints substantially improves binding free-energy predictions.
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Affiliation(s)
- Abir Ganguly
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Hsu-Chun Tsai
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Mario Fernández-Pendás
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
- Donostia International Physics Center (DIPC), PK 1072, 20080 Donostia-San Sebastian, Spain
| | - Tai-Sung Lee
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Timothy J. Giese
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Darrin M. York
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
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17
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Adsorption of oleic acid on magnetite facets. Commun Chem 2022; 5:134. [PMID: 36697717 PMCID: PMC9814498 DOI: 10.1038/s42004-022-00741-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 09/26/2022] [Indexed: 01/28/2023] Open
Abstract
The microscopic understanding of the atomic structure and interaction at carboxylic acid/oxide interfaces is an important step towards tailoring the mechanical properties of nanocomposite materials assembled from metal oxide nanoparticles functionalized by organic molecules. We have studied the adsorption of oleic acid (C17H33COOH) on the most prominent magnetite (001) and (111) crystal facets at room temperature using low energy electron diffraction, surface X-ray diffraction and infrared vibrational spectroscopy complemented with molecular dynamics simulations used to infer specific hydrogen bonding motifs between oleic acid and oleate. Our experimental and theoretical results give evidence that oleic acid adsorbs dissociatively on both facets at lower coverages. At higher coverages, the more pronounced molecular adsorption causes hydrogen bond formation between the carboxylic groups, leading to a more upright orientation of the molecules on the (111) facet in conjunction with the formation of a denser layer, as compared to the (001) facet. This is evidenced by the C=O double bond infrared line shape, in depth molecular dynamics bond angle orientation and hydrogen bond analysis, as well as X-ray reflectivity layer electron density profile determination. Such a higher density can explain the higher mechanical strength of nanocomposite materials based on magnetite nanoparticles with larger (111) facets.
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18
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Lundborg M, Wennberg C, Lidmar J, Hess B, Lindahl E, Norlén L. Skin permeability prediction with MD simulation sampling spatial and alchemical reaction coordinates. Biophys J 2022; 121:3837-3849. [PMID: 36104960 PMCID: PMC9674988 DOI: 10.1016/j.bpj.2022.09.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/22/2022] [Accepted: 09/08/2022] [Indexed: 11/02/2022] Open
Abstract
A molecular-level understanding of skin permeation may rationalize and streamline product development, and improve quality and control, of transdermal and topical drug delivery systems. It may also facilitate toxicity and safety assessment of cosmetics and skin care products. Here, we present new molecular dynamics simulation approaches that make it possible to efficiently sample the free energy and local diffusion coefficient across the skin's barrier structure to predict skin permeability and the effects of chemical penetration enhancers. In particular, we introduce a new approach to use two-dimensional reaction coordinates in the accelerated weight histogram method, where we combine sampling along spatial coordinates with an alchemical perturbation virtual coordinate. We present predicted properties for 20 permeants, and demonstrate how our approach improves correlation with ex vivo/in vitro skin permeation data. For the compounds included in this study, the obtained log KPexp-calc mean square difference was 0.9 cm2 h-2.
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Affiliation(s)
| | | | - Jack Lidmar
- Department of Physics, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Berk Hess
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden
| | - Erik Lindahl
- Department of Biophysics and Biochemistry, Science for Life Laboratory, Stockholm University, Solna, Sweden; Department of Physics, Swedish e-Science Research Center, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Lars Norlén
- Department of Cell and Molecular Biology (CMB), Karolinska Institutet, Stockholm, Sweden; Dermatology Clinic, Karolinska University Hospital, Stockholm, Sweden.
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19
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Westerlund AM, Sridhar A, Dahl L, Andersson A, Bodnar AY, Delemotte L. Markov state modelling reveals heterogeneous drug-inhibition mechanism of Calmodulin. PLoS Comput Biol 2022; 18:e1010583. [PMID: 36206305 PMCID: PMC9581412 DOI: 10.1371/journal.pcbi.1010583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 10/19/2022] [Accepted: 09/18/2022] [Indexed: 11/06/2022] Open
Abstract
Calmodulin (CaM) is a calcium sensor which binds and regulates a wide range of target-proteins. This implicitly enables the concentration of calcium to influence many downstream physiological responses, including muscle contraction, learning and depression. The antipsychotic drug trifluoperazine (TFP) is a known CaM inhibitor. By binding to various sites, TFP prevents CaM from associating to target-proteins. However, the molecular and state-dependent mechanisms behind CaM inhibition by drugs such as TFP are largely unknown. Here, we build a Markov state model (MSM) from adaptively sampled molecular dynamics simulations and reveal the structural and dynamical features behind the inhibitory mechanism of TFP-binding to the C-terminal domain of CaM. We specifically identify three major TFP binding-modes from the MSM macrostates, and distinguish their effect on CaM conformation by using a systematic analysis protocol based on biophysical descriptors and tools from machine learning. The results show that depending on the binding orientation, TFP effectively stabilizes features of the calcium-unbound CaM, either affecting the CaM hydrophobic binding pocket, the calcium binding sites or the secondary structure content in the bound domain. The conclusions drawn from this work may in the future serve to formulate a complete model of pharmacological modulation of CaM, which furthers our understanding of how these drugs affect signaling pathways as well as associated diseases. Calmodulin (CaM) is a calcium-sensing protein which makes other proteins dependent on the surrounding calcium concentration by binding to these proteins. Such protein-protein interactions with CaM are vital for calcium to control many physiological pathways within the cell. The antipsychotic drug trifluoperazine (TFP) inhibits CaM’s ability to bind and regulate other proteins. Here, we use molecular dynamics simulations together with Markov state modeling and machine learning to understand the structural and dynamical features by which TFP bound to the one domain of CaM prevents association to other proteins. We find that TFP encourages CaM to adopt a conformation that is like the one stabilized in absence of calcium: depending on the binding orientation of TFP, the drug indeed either affects the CaM hydrophobic binding pocket, the calcium binding sites or the secondary structure content in the domain. Understanding TFP binding is a first step towards designing better drugs targeting CaM.
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Affiliation(s)
- Annie M. Westerlund
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden
| | - Akshay Sridhar
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden
| | - Leo Dahl
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden
| | - Alma Andersson
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden
- Division of Gene Technology, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Anna-Yaroslava Bodnar
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden
| | - Lucie Delemotte
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden
- * E-mail:
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20
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Brankin AE, Fowler PW. Predicting antibiotic resistance in complex protein targets using alchemical free energy methods. J Comput Chem 2022; 43:1771-1782. [PMID: 36054249 PMCID: PMC9545121 DOI: 10.1002/jcc.26979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 07/26/2022] [Accepted: 07/26/2022] [Indexed: 11/10/2022]
Abstract
Drug resistant Mycobacterium tuberculosis, which mostly results from single nucleotide polymorphisms in antibiotic target genes, poses a major threat to tuberculosis treatment outcomes. Relative binding free energy (RBFE) calculations can rapidly predict the effects of mutations, but this approach has not been tested on large, complex proteins. We use RBFE calculations to predict the effects of M. tuberculosis RNA polymerase and DNA gyrase mutations on rifampicin and moxifloxacin susceptibility respectively. These mutations encompass a range of amino acid substitutions with known effects and include large steric perturbations and charged moieties. We find that moderate numbers (n = 3-15) of short RBFE calculations can predict resistance in cases where the mutation results in a large change in the binding free energy. We show that the method lacks discrimination in cases with either a small change in energy or that involve charged amino acids, and we investigate how these calculation errors may be decreased.
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Affiliation(s)
- Alice E. Brankin
- Nuffield Department of Medicine, John Radcliffe HospitalUniversity of OxfordOxfordUK
| | - Philip W. Fowler
- Nuffield Department of Medicine, John Radcliffe HospitalUniversity of OxfordOxfordUK
- National Institute of Health Research Oxford Biomedical Research CentreJohn Radcliffe HospitalOxfordUK
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21
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Oliveira MP, Gonçalves YMH, Ol Gheta SK, Rieder SR, Horta BAC, Hünenberger PH. Comparison of the United- and All-Atom Representations of (Halo)alkanes Based on Two Condensed-Phase Force Fields Optimized against the Same Experimental Data Set. J Chem Theory Comput 2022; 18:6757-6778. [PMID: 36190354 DOI: 10.1021/acs.jctc.2c00524] [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 level of accuracy that can be achieved by a force field is influenced by choices made in the interaction-function representation and in the relevant simulation parameters. These choices, referred to here as functional-form variants (FFVs), include for example the model resolution, the charge-derivation procedure, the van der Waals combination rules, the cutoff distance, and the treatment of the long-range interactions. Ideally, assessing the effect of a given FFV on the intrinsic accuracy of the force-field representation requires that only the specific FFV is changed and that this change is performed at an optimal level of parametrization, a requirement that may prove extremely challenging to achieve in practice. Here, we present a first attempt at such a comparison for one specific FFV, namely the choice of a united-atom (UA) versus an all-atom (AA) resolution in a force field for saturated acyclic (halo)alkanes. Two force-field versions (UA vs AA) are optimized in an automated way using the CombiFF approach against 961 experimental values for the pure-liquid densities ρliq and vaporization enthalpies ΔHvap of 591 compounds. For the AA force field, the torsional and third-neighbor Lennard-Jones parameters are also refined based on quantum-mechanical rotational-energy profiles. The comparison between the UA and AA resolutions is also extended to properties that have not been included as parameterization targets, namely the surface-tension coefficient γ, the isothermal compressibility κT, the isobaric thermal-expansion coefficient αP, the isobaric heat capacity cP, the static relative dielectric permittivity ϵ, the self-diffusion coefficient D, the shear viscosity η, the hydration free energy ΔGwat, and the free energy of solvation ΔGche in cyclohexane. For the target properties ρliq and ΔHvap, the UA and AA resolutions reach very similar levels of accuracy after optimization. For the nine other properties, the AA representation leads to more accurate results in terms of η; comparably accurate results in terms of γ, κT, αP, ϵ, D, and ΔGche; and less accurate results in terms of cP and ΔGwat. This work also represents a first step toward the calibration of a GROMOS-compatible force field at the AA resolution.
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Affiliation(s)
- Marina P Oliveira
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Yan M H Gonçalves
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - S Kashef Ol Gheta
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Salomé R Rieder
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Bruno A C Horta
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Philippe H Hünenberger
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
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22
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Kabedev A, Zhuo X, Leng D, Foderà V, Zhao M, Larsson P, Bergström CAS, Löbmann K. Stabilizing Mechanisms of β-Lactoglobulin in Amorphous Solid Dispersions of Indomethacin. Mol Pharm 2022; 19:3922-3933. [PMID: 36135343 DOI: 10.1021/acs.molpharmaceut.2c00397] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Proteins, and in particular whey proteins, have recently been introduced as a promising excipient class for stabilizing amorphous solid dispersions. However, despite the efficacy of the approach, the molecular mechanisms behind the stabilization of the drug in the amorphous form are not yet understood. To investigate these, we used experimental and computational techniques to study the impact of drug loading on the stability of protein-stabilized amorphous formulations. β-Lactoglobulin, a major component of whey, was chosen as a model protein and indomethacin as a model drug. Samples, prepared by either ball milling or spray drying, formed single-phase amorphous solid dispersions with one glass transition temperature at drug loadings lower than 40-50%; however, a second glass transition temperature appeared at drug loadings higher than 40-50%. Using molecular dynamics simulations, we found that a drug-rich phase occurred at a loading of 40-50% and higher, in agreement with the experimental data. The simulations revealed that the mechanisms of the indomethacin stabilization by β-lactoglobulin were a combination of (a) reduced mobility of the drug molecules in the first drug shell and (b) hydrogen-bond networks. These networks, formed mostly by glutamic and aspartic acids, are situated at the β-lactoglobulin surface, and dependent on the drug loading (>40%), propagated into the second and subsequent drug layers. The simulations indicate that the reduced mobility dominates at low (<40%) drug loadings, whereas hydrogen-bond networks dominate at loadings up to 75%. The computer simulation results agreed with the experimental physical stability data, which showed a significant stabilization effect up to a drug fraction of 70% under dry storage. However, under humid conditions, stabilization was only sufficient for drug loadings up to 50%, confirming the detrimental effect of humidity on the stability of protein-stabilized amorphous formulations.
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Affiliation(s)
- Aleksei Kabedev
- Department of Pharmacy, Uppsala University, 75123 Uppsala, Sweden
| | - Xuezhi Zhuo
- Department of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Donglei Leng
- Zerion Pharma A/S, Blokken 11, 3460 Birkerød, Denmark
| | - Vito Foderà
- Department of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Min Zhao
- School of Pharmacy, Queen's University Belfast, Belfast BT9 7BL, U.K.,Queen's University Belfast Joint College (CQC), China Medical University, Shenyang 110000, China
| | - Per Larsson
- Department of Pharmacy, Uppsala University, 75123 Uppsala, Sweden
| | | | - Korbinian Löbmann
- Department of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark.,Zerion Pharma A/S, Blokken 11, 3460 Birkerød, Denmark
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23
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Abstract
Generalized force fields (FFs) act as extensions to biomolecular FFs to provide a wide coverage of organic molecules. However, their precise application to an arbitrary molecule presents a separate challenge. We show that MATCH assigns different atom types and bonded and nonbonded parameters than CGenFF, and the AM1-BCC charge model, commonly used with GAFF/GAFF2, does not exactly reproduce the performance of the RESP charge model. The results indicate the need for caution when employing FFs to ensure their integrity with respect to their implementation and validation.
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Affiliation(s)
- Asuka A. Orr
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
| | - Suliman Sharif
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
| | - Junmei Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
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24
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Screening of Potential Breast Cancer Inhibitors through Molecular Docking and Molecular Dynamics Simulation. BIOMED RESEARCH INTERNATIONAL 2022; 2022:3338549. [PMID: 35800218 PMCID: PMC9256436 DOI: 10.1155/2022/3338549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/25/2022] [Accepted: 06/06/2022] [Indexed: 11/17/2022]
Abstract
Cyclooxygenase-2 (COX-2) is a key enzyme involved in overexpression in several human cancerous diseases including breast cancer. By performing efficient virtual screening in a series of active molecules or compounds from the Maybridge, NCI (National Cancer Institute), and Enamine databases, potential identification of COX-2 inhibitors could lead to new prognostic strategies in the treatment of breast cancer. Based on a 50% structural similitude, compounds were chosen as the inductive model of COX-2 inhibitions from these databases. Selected compounds were filtered and tested with Lipinski’s rule of five followed by absorption, distribution, metabolism, and excretion (ADME) properties. Subsequently, molecular docking was performed to achieve accuracy in screening and also to find an interactive mechanism between hit compounds with their respective binding sites. Simultaneously, molecular simulations of top-scored compounds were selected and coded such as Maybridge_55417, NCI_30552, and Enamine_62410. Chosen compounds were analyzed and interpreted with COX-2 affinity. Results endorsed that hydrophobic affinity and optimum hydrogen bonds were the forces driven in the interactive mechanism of in silico hits compounds with COX-2 and can be used as efficient alternative therapeutic agents targeting deleterious breast cancer. With these in silico findings, compounds identified may prevent the action of the COX-2 enzyme and thereby diminish the incidence of breast cancer.
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25
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Soliman ME, Adewumi AT, Akawa OB, Subair TI, Okunlola FO, Akinsuku OE, Khan S. Simulation Models for Prediction of Bioavailability of Medicinal Drugs-the Interface Between Experiment and Computation. AAPS PharmSciTech 2022; 23:86. [PMID: 35292867 DOI: 10.1208/s12249-022-02229-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 02/03/2022] [Indexed: 12/17/2022] Open
Abstract
The oral drug bioavailability (BA) problems have remained inevitable over the years, impairing drug efficacy and indirectly leading to eventual human morbidity and mortality. However, some conventional lab-based methods improve drug absorption leading to enhanced BA, and the recent experimental techniques are up-and-coming. Nevertheless, some have inherent drawbacks in improving the efficacy of poorly insoluble and low impermeable drugs. Drug BA and strategies to overcome these challenges were briefly highlighted. This review has significantly unravelled the different computational models for studying and predicting drug bioavailability. Several computational approaches provide mechanistic insights into the oral drug delivery system simulation of descriptors like solubility, permeability, transport protein-ligand interactions, and molecular structures. The in silico techniques have long been known still are just being applied to unravel drug bioavailability issues. Many publications have reported novel applications of the computational models towards achieving improved drug BA, including predicting gastrointestinal tract (GIT) drug absorption properties and passive intestinal membrane permeability, thus maximizing time and resources. Also, the classical molecular simulation models for free solvation energies of soluble-related processes such as solubilization, dissolutions, supersaturation, and precipitation have been used in virtual screening studies. A few of the tools are GastroPlusTM that supports biowaiver for drugs, mainly BCS class III and predicts drug compounds' absorption and pharmacokinetic process; SimCyp® simulator for mechanistic modelling and simulation of drug formulation processes; pharmacodynamics analysis on non-linear mixed-effects modelling; and mathematical models, predicting absorption potential/maximum absorption dose. This review provides in silico-experiment annexation in the drug bioavailability enhancement, possible insights that lead to critical opinion on the applications and reliability of the various in silico models as a growing tool for drug development and discovery, thus accelerating drug development processes.
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26
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Alencar WLM, da Silva Arouche T, Neto AFG, de Castro Ramalho T, de Carvalho Júnior RN, de Jesus Chaves Neto AM. Interactions of Co, Cu, and non-metal phthalocyanines with external structures of SARS-CoV-2 using docking and molecular dynamics. Sci Rep 2022; 12:3316. [PMID: 35228662 PMCID: PMC8885651 DOI: 10.1038/s41598-022-07396-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 02/10/2022] [Indexed: 02/06/2023] Open
Abstract
The new coronavirus, SARS-CoV-2, caused the COVID-19 pandemic, characterized by its high rate of contamination, propagation capacity, and lethality rate. In this work, we approach the use of phthalocyanines as an inhibitor of SARS-CoV-2, as they present several interactive properties of the phthalocyanines (Pc) of Cobalt (CoPc), Copper (CuPc) and without a metal group (NoPc) can interact with SARS-CoV-2, showing potential be used as filtering by adsorption on paints on walls, masks, clothes, and air conditioning filters. Molecular modeling techniques through Molecular Docking and Molecular Dynamics were used, where the target was the external structures of the virus, but specifically the envelope protein, main protease, and Spike glycoprotein proteases. Using the g_MM-GBSA module and with it, the molecular docking studies show that the ligands have interaction characteristics capable of adsorbing the structures. Molecular dynamics provided information on the root-mean-square deviation of the atomic positions provided values between 1 and 2.5. The generalized Born implicit solvation model, Gibbs free energy, and solvent accessible surface area approach were used. Among the results obtained through molecular dynamics, it was noticed that interactions occur since Pc could bind to residues of the active site of macromolecules, demonstrating good interactions; in particular with CoPc. Molecular couplings and free energy showed that S-gly active site residues interacted strongly with phthalocyanines with values of - 182.443 kJ/mol (CoPc), 158.954 kJ/mol (CuPc), and - 129.963 kJ/mol (NoPc). The interactions of Pc's with SARS-CoV-2 may predict some promising candidates for antagonists to the virus, which if confirmed through experimental approaches, may contribute to resolving the global crisis of the COVID-19 pandemic.
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Affiliation(s)
- Wilson Luna Machado Alencar
- Laboratory of Preparation and Computation of Nanomaterials (LPCN), Federal University of Pará, C. P. 479, Belem, PA, 66075-110, Brazil
- Pos-Graduation Program in Engineering of Natural Resources of the Amazon, ITEC, Federal University of Pará, C. P. 2626, Belém, PA, 66050-540, Brazil
- Federal Institute of Pará (IFPA), C. P. BR 316, Km 61, Castanhal, PA, 68740-970, Brazil
| | - Tiago da Silva Arouche
- Laboratory of Preparation and Computation of Nanomaterials (LPCN), Federal University of Pará, C. P. 479, Belem, PA, 66075-110, Brazil
| | | | | | - Raul Nunes de Carvalho Júnior
- Pos-Graduation Program in Engineering of Natural Resources of the Amazon, ITEC, Federal University of Pará, C. P. 2626, Belém, PA, 66050-540, Brazil
- Pos-Graduation Program in Chemical Engineering, ITEC, Federal University of Pará, C. P. 479, Belém, PA, 66075-900, Brazil
| | - Antonio Maia de Jesus Chaves Neto
- Laboratory of Preparation and Computation of Nanomaterials (LPCN), Federal University of Pará, C. P. 479, Belem, PA, 66075-110, Brazil.
- Pos-Graduation Program in Engineering of Natural Resources of the Amazon, ITEC, Federal University of Pará, C. P. 2626, Belém, PA, 66050-540, Brazil.
- Pos-Graduation Program in Chemical Engineering, ITEC, Federal University of Pará, C. P. 479, Belém, PA, 66075-900, Brazil.
- National Professional Master's in Physics Teaching, Federal University of Pará, C. P. 479, Belém, PA, 66075-110, Brazil.
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27
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Rama P, Abbas Z. The influence of silica nanoparticle geometry on the interfacial interactions of organic molecules: a molecular dynamics study. Phys Chem Chem Phys 2022; 24:3713-3721. [PMID: 35080551 DOI: 10.1039/d1cp04315c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The role of nanoparticle shape in the interaction and adsorption of organic molecules on the particle surface is an unexplored area. On the other hand, such knowledge is not only vital for a basic understanding of organic molecule interaction with nanoparticle surfaces but also essential for evaluating the cellular uptake of nanoparticles for living organisms. The current study investigates the role of silica nanoparticle shape in the interactions of phthalic acid organic molecules by using molecular dynamics simulations. Silica nanoparticles of two different geometries namely spheroid and cuboid with varying charge densities along with protonated and deprotonated phthalic acid molecules are studied. The adsorption characteristics of phthalic acid molecules on these nanoparticles have been analysed under different aquatic environments. The interactions of phthalic acid molecules, water molecules and ions were found to be different for spheroid and cubic shaped particles at pH values of 2-3, 7 and 9-10. The interaction of phthalic acid molecules with cubical silica nanoparticles is enhanced compared to the spherical shape particles. Such an enhanced interaction was seen when the silica surface is neutral, pH 2-3 and when the silica surface is charged at pH 7 and pH 9-10 in the presence of 0.5 M NaCl electrolyte. The cuboid-shaped silica also exhibited more hydrophilicity and less negative surface potential compared to spheroid shaped particles at pH 9-10. This is due to the enhanced condensation of Na+ counter-ions at the cuboid nanoparticle solution interface as to the interface of spheroid particles, which is well in agreement with Manning's theory of counter-ion condensation. Simulation results presented in this study indicate that the shape of the silica nanoparticle has significant influence on the interaction of water molecules, counter-ions and organic molecules which consequently determine the adsorption behaviour of organic molecules on the nanoparticle surface.
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Affiliation(s)
- Prasad Rama
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg - 41125, Sweden.
| | - Zareen Abbas
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg - 41125, Sweden.
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28
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Gao S, Bao X, Yu L, Wang H, Li J, Chen X. Molecular dynamics study of “quasi-gemini” surfactant at n-decane/water interface: The synergistic effect of hydrophilic headgroups and hydrophobic tails of surfactants on the interface properties. Colloids Surf A Physicochem Eng Asp 2022. [DOI: 10.1016/j.colsurfa.2021.127899] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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29
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Li L, Wang Z, Liu J, Chen J, Jin X, Dai C. Synthesis and Performance Evaluation of Polyhydroxy Benzene Sulfonate Oil Displacement Agent Based on Enhanced Interfacial Wettability Control. ACTA CHIMICA SINICA 2022. [DOI: 10.6023/a21080413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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30
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Edueng K, Kabedev A, Ekdahl A, Mahlin D, Baumann J, Mudie D, Bergström CAS. Pharmaceutical profiling and molecular dynamics simulations reveal crystallization effects in amorphous formulations. Int J Pharm 2021; 613:121360. [PMID: 34896563 DOI: 10.1016/j.ijpharm.2021.121360] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 11/30/2021] [Accepted: 12/04/2021] [Indexed: 10/19/2022]
Abstract
Robust and reliable in vivo performance of medicines based on amorphous solid dispersions (ASDs) depend on maintenance of physical stability and efficient supersaturation. However, molecular drivers of these two kinetic processes are poorly understood. Here we used molecular dynamics (MD) simulations coupled with experimental assessments to explore supersaturation, nucleation, and crystal growth. The effect of drug loading on physical stability and supersaturation potential was highly drug specific. Storage under humid conditions influenced crystallization, but also resulted in morphological changes and particle fusion. This led to increased particle size, which significantly reduced dissolution rate. MD simulations identified the importance of nano-compartmentalization in the crystallization rate of the ASDs. Nucleation during storage did not inherently compromise the ASD. Rather, the poorer performance resulted from a combination of properties of the compound, nanostructures formed in the formulation, and crystallization.
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Affiliation(s)
- Khadijah Edueng
- Department of Pharmacy, Uppsala University, Husargatan 3, 75 123 Uppsala, Sweden
| | - Aleksei Kabedev
- Department of Pharmacy, Uppsala University, Husargatan 3, 75 123 Uppsala, Sweden
| | - Alyssa Ekdahl
- Cockrell School of Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| | - Denny Mahlin
- Department of Pharmacy, Uppsala University, Husargatan 3, 75 123 Uppsala, Sweden; AstraZeneca Operations, Forskargatan 18, 151 85 Södertälje, Sweden
| | - John Baumann
- Global Research and Development, Lonza, Bend, OR 97703, USA
| | - Deanna Mudie
- Global Research and Development, Lonza, Bend, OR 97703, USA
| | - Christel A S Bergström
- Department of Pharmacy, Uppsala University, Husargatan 3, 75 123 Uppsala, Sweden; The Swedish Drug Delivery Center, Department of Pharmacy, Uppsala University, Husargatan 3, 75123 Uppsala, Sweden.
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31
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Li P, Li Z, Wang Y, Dou H, Radak BK, Allen BK, Sherman W, Xu H. Precise Binding Free Energy Calculations for Multiple Molecules Using an Optimal Measurement Network of Pairwise Differences. J Chem Theory Comput 2021; 18:650-663. [PMID: 34871502 DOI: 10.1021/acs.jctc.1c00703] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Alchemical binding free energy (BFE) calculations offer an efficient and thermodynamically rigorous approach to in silico binding affinity predictions. As a result of decades of methodological improvements and recent advances in computer technology, alchemical BFE calculations are now widely used in drug discovery research. They help guide the prioritization of candidate drug molecules by predicting their binding affinities for a biomolecular target of interest (and potentially selectivity against undesirable antitargets). Statistical variance associated with such calculations, however, may undermine the reliability of their predictions, introducing uncertainty both in ranking candidate molecules and in benchmarking their predictive accuracy. Here, we present a computational method that substantially improves the statistical precision in BFE calculations for a set of ligands binding to a common receptor by dynamically allocating computational resources to different BFE calculations according to an optimality objective established in a previous work from our group and extended in this work. Our method, termed Network Binding Free Energy (NetBFE), performs adaptive BFE calculations in iterations, re-optimizing the allocations in each iteration based on the statistical variances estimated from previous iterations. Using examples of NetBFE calculations for protein binding of congeneric ligand series, we demonstrate that NetBFE approaches the optimal allocation in a small number (≤5) of iterations and that NetBFE reduces the statistical variance in the BFE estimates by approximately a factor of 2 when compared to a previously published and widely used allocation method at the same total computational cost.
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Affiliation(s)
- Pengfei Li
- Silicon Therapeutics, Suzhou, Jiangsu 215000, China
| | - Zhijie Li
- Silicon Therapeutics, Suzhou, Jiangsu 215000, China
| | - Yu Wang
- Silicon Therapeutics, Suzhou, Jiangsu 215000, China
| | - Huaixia Dou
- Silicon Therapeutics, Suzhou, Jiangsu 215000, China
| | - Brian K Radak
- Roivant Sciences, Boston, Massachusetts 02210, United States
| | - Bryce K Allen
- Silicon Therapeutics, Boston, Massachusetts 02210, United States
| | - Woody Sherman
- Roivant Sciences, Boston, Massachusetts 02210, United States
| | - Huafeng Xu
- Roivant Sciences, New York, New York 10036, United States
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32
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Lundborg M, Lidmar J, Hess B. The accelerated weight histogram method for alchemical free energy calculations. J Chem Phys 2021; 154:204103. [PMID: 34241154 DOI: 10.1063/5.0044352] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The accelerated weight histogram method is an enhanced sampling technique used to explore free energy landscapes by applying an adaptive bias. The method is general and easy to extend. Herein, we show how it can be used to efficiently sample alchemical transformations, commonly used for, e.g., solvation and binding free energy calculations. We present calculations and convergence of the hydration free energy of testosterone, representing drug-like molecules. We also include methane and ethanol to validate the results. The protocol is easy to use, does not require a careful choice of parameters, and scales well to accessible resources, and the results converge at least as quickly as when using conventional methods. One benefit of the method is that it can easily be combined with other reaction coordinates, such as intermolecular distances.
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Affiliation(s)
| | - J Lidmar
- Department of Physics, KTH Royal Institute of Technology, 10691 Stockholm, Sweden
| | - B Hess
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, 10691 Stockholm, Sweden
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33
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Fan S, Nedev H, Vijayan R, Iorga BI, Beckstein O. Precise force-field-based calculations of octanol-water partition coefficients for the SAMPL7 molecules. J Comput Aided Mol Des 2021; 35:853-870. [PMID: 34232435 PMCID: PMC8397498 DOI: 10.1007/s10822-021-00407-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 06/22/2021] [Indexed: 10/20/2022]
Abstract
We predicted water-octanol partition coefficients for the molecules in the SAMPL7 challenge with explicit solvent classical molecular dynamics (MD) simulations. Water hydration free energies and octanol solvation free energies were calculated with a windowed alchemical free energy approach. Three commonly used force fields (AMBER GAFF, CHARMM CGenFF, OPLS-AA) were tested. Special emphasis was placed on converging all simulations, using a criterion developed for the SAMPL6 challenge. In aggregate, over 1000 [Formula: see text]s of simulations were performed, with some free energy windows remaining not fully converged even after 1 [Formula: see text]s of simulation time. Nevertheless, the amount of sampling produced [Formula: see text] estimates with a precision of 0.1 log units or better for converged simulations. Despite being probably as fully sampled as can expected and is feasible, the agreement with experiment remained modest for all force fields, with no force field performing better than 1.6 in root mean squared error. Overall, our results indicate that a large amount of sampling is necessary to produce precise [Formula: see text] predictions for the SAMPL7 compounds and that high precision does not necessarily lead to high accuracy. Thus, fundamental problems remain to be solved for physics-based [Formula: see text] predictions.
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Affiliation(s)
- Shujie Fan
- Department of Physics, Arizona State University, P.O. Box 871504, Tempe, AZ, 85287-1504, USA
| | - Hristo Nedev
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, Labex LERMIT, 1 Avenue de la Terrasse, 91198, Gif-sur-Yvette, France
| | - Ranjit Vijayan
- Department of Biology, College of Science, United Arab Emirates University, PO Box 15551, Al Ain, UAE
| | - Bogdan I Iorga
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, Labex LERMIT, 1 Avenue de la Terrasse, 91198, Gif-sur-Yvette, France.
| | - Oliver Beckstein
- Department of Physics and Center for Biological Physics, Arizona State University, P.O. Box 871504, Tempe, AZ, 85287-1504, USA.
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34
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Kashefolgheta S, Wang S, Acree WE, Hünenberger PH. Evaluation of nine condensed-phase force fields of the GROMOS, CHARMM, OPLS, AMBER, and OpenFF families against experimental cross-solvation free energies. Phys Chem Chem Phys 2021; 23:13055-13074. [PMID: 34105547 PMCID: PMC8207520 DOI: 10.1039/d1cp00215e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 04/28/2021] [Indexed: 12/02/2022]
Abstract
Experimental solvation free energies are nowadays commonly included as target properties in the validation of condensed-phase force fields, sometimes even in their calibration. In a previous article [Kashefolgheta et al., J. Chem. Theory. Comput., 2020, 16, 7556-7580], we showed how the involved comparison between experimental and simulation results could be made more systematic by considering a full matrix of cross-solvation free energies . For a set of N molecules that are all in the liquid state under ambient conditions, such a matrix encompasses N×N entries for considering each of the N molecules either as solute (A) or as solvent (B). In the quoted study, a cross-solvation matrix of 25 × 25 experimental value was introduced, considering 25 small molecules representative for alkanes, chloroalkanes, ethers, ketones, esters, alcohols, amines, and amides. This experimental data was used to compare the relative accuracies of four popular condensed-phase force fields, namely GROMOS-2016H66, OPLS-AA, AMBER-GAFF, and CHARMM-CGenFF. In the present work, the comparison is extended to five additional force fields, namely GROMOS-54A7, GROMOS-ATB, OPLS-LBCC, AMBER-GAFF2, and OpenFF. Considering these nine force fields, the correlation coefficients between experimental values and simulation results range from 0.76 to 0.88, the root-mean-square errors (RMSEs) from 2.9 to 4.8 kJ mol-1, and average errors (AVEEs) from -1.5 to +1.0 kJ mol-1. In terms of RMSEs, GROMOS-2016H66 and OPLS-AA present the best accuracy (2.9 kJ mol-1), followed by OPLS-LBCC, AMBER-GAFF2, AMBER-GAFF, and OpenFF (3.3 to 3.6 kJ mol-1), and then by GROMOS-54A7, CHARM-CGenFF, and GROMOS-ATB (4.0 to 4.8 kJ mol-1). These differences are statistically significant but not very pronounced, and are distributed rather heterogeneously over the set of compounds within the different force fields.
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Affiliation(s)
- Sadra Kashefolgheta
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCICH-8093 ZürichSwitzerland+41 44 632 55 03
| | - Shuzhe Wang
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCICH-8093 ZürichSwitzerland+41 44 632 55 03
| | - William E. Acree
- Department of Chemistry, University of North Texas1155 Union Circle Drive #305070DentonTexas 76203USA
| | - Philippe H. Hünenberger
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCICH-8093 ZürichSwitzerland+41 44 632 55 03
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Dutta S, Corni S, Brancolini G. Molecular Dynamics Simulations of a Catalytic Multivalent Peptide-Nanoparticle Complex. Int J Mol Sci 2021; 22:3624. [PMID: 33807225 PMCID: PMC8037132 DOI: 10.3390/ijms22073624] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/22/2021] [Accepted: 03/25/2021] [Indexed: 11/16/2022] Open
Abstract
Molecular modeling of a supramolecular catalytic system is conducted resulting from the assembling between a small peptide and the surface of cationic self-assembled monolayers on gold nanoparticles, through a multiscale iterative approach including atomistic force field development, flexible docking with Brownian Dynamics and µs-long Molecular Dynamics simulations. Self-assembly is a prerequisite for the catalysis, since the catalytic peptides do not display any activity in the absence of the gold nanocluster. Atomistic simulations reveal details of the association dynamics as regulated by defined conformational changes of the peptide due to peptide length and sequence. Our results show the importance of a rational design of the peptide to enhance the catalytic activity of peptide-nanoparticle conjugates and present a viable computational approach toward the design of enzyme mimics having a complex structure-function relationship, for technological and nanomedical applications.
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Affiliation(s)
- Sutapa Dutta
- Dipartimento di Scienze Chimiche, Università di Padova, 35131 Padova, Italy;
- Istituto Nanoscienze, CNR-NANO S3, via G. Campi 213/A, 41125 Modena, Italy
| | - Stefano Corni
- Dipartimento di Scienze Chimiche, Università di Padova, 35131 Padova, Italy;
- Istituto Nanoscienze, CNR-NANO S3, via G. Campi 213/A, 41125 Modena, Italy
| | - Giorgia Brancolini
- Istituto Nanoscienze, CNR-NANO S3, via G. Campi 213/A, 41125 Modena, Italy
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Al-Sanea MM, Obaidullah AJ, Shaker ME, Chilingaryan G, Alanazi MM, Alsaif NA, Alkahtani HM, Alsubaie SA, Abdelgawad MA. A New CDK2 Inhibitor with 3-Hydrazonoindolin-2-One Scaffold Endowed with Anti-Breast Cancer Activity: Design, Synthesis, Biological Evaluation, and In Silico Insights. Molecules 2021; 26:molecules26020412. [PMID: 33466812 PMCID: PMC7830330 DOI: 10.3390/molecules26020412] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/08/2021] [Accepted: 01/11/2021] [Indexed: 12/18/2022] Open
Abstract
Background: Cyclin-dependent kinases (CDKs) regulate mammalian cell cycle progression and RNA transcription. Based on the structural analysis of previously reported CDK2 inhibitors, a new compound with 3-hydrazonoindolin-2-one scaffold (HI 5) was well designed, synthesized, and biologically evaluated as a promising anti-breast cancer hit compound. Methods: The potential anti-cancerous effect of HI 5 was evaluated using cytotoxicity assay, flow cytometric analysis of apoptosis and cell cycle distribution, ELISA immunoassay, in vitro CDK2/cyclin A2 activity, and molecular operating environment (MOE) virtual docking studies. Results: The results revealed that HI 5 exhibits pronounced CDK2 inhibitory activity and cytotoxicity in human breast cancer MCF-7 cell line. The cytotoxicity of HI 5 was found to be intrinsically mediated apoptosis, which in turn, is associated with low Bcl-2 expression and high activation of caspase 3 and p53. Besides, HI 5 blocked the proliferation of the MCF-7 cell line and arrested the cell cycle at the G2/M phase. The docking studies did not confirm which one of geometric isomers (syn and anti) is responsible for binding affinity and intrinsic activity of HI 5. However, the molecular dynamic studies have confirmed that the syn-isomer has more favorable binding interaction and thus is responsible for CDK2 inhibitory activity. Discussion: These findings displayed a substantial basis of synthesizing further derivatives based on the 3-hydrazonoindolin-2-one scaffold for favorable targeting of breast cancer.
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Affiliation(s)
- Mohammad M. Al-Sanea
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka 72341, Aljouf Province, Saudi Arabia;
- Correspondence: (M.M.A.-S.); (A.J.O.); Tel.: +966-594076460 (M.M.A.-S.)
| | - Ahmad J. Obaidullah
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (M.M.A.); (N.A.A.); (H.M.A.); (S.A.A.)
- Correspondence: (M.M.A.-S.); (A.J.O.); Tel.: +966-594076460 (M.M.A.-S.)
| | - Mohamed E. Shaker
- Department of Pharmacology, College of Pharmacy, Jouf University, Sakaka, Aljouf 72341, Saudi Arabia;
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Garri Chilingaryan
- Institute of Biomedicine and Pharmacy, Russian-Armenian University, Yerevan 0051, Armenia;
| | - Mohammed M. Alanazi
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (M.M.A.); (N.A.A.); (H.M.A.); (S.A.A.)
| | - Nawaf A. Alsaif
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (M.M.A.); (N.A.A.); (H.M.A.); (S.A.A.)
| | - Hamad M. Alkahtani
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (M.M.A.); (N.A.A.); (H.M.A.); (S.A.A.)
| | - Sultan A. Alsubaie
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (M.M.A.); (N.A.A.); (H.M.A.); (S.A.A.)
| | - Mohamed A. Abdelgawad
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka 72341, Aljouf Province, Saudi Arabia;
- Department of Pharmaceutical Organic Chemistry, Beni-Suef University, Beni-Suef 62514, Egypt
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Lewis-Atwell T, Townsend PA, Grayson MN. Comparisons of different force fields in conformational analysis and searching of organic molecules: A review. Tetrahedron 2021. [DOI: 10.1016/j.tet.2020.131865] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Rogers TR, Wang F. Accurate MP2-based force fields predict hydration free energies for simple alkanes and alcohols in good agreement with experiments. J Chem Phys 2020; 153:244505. [PMID: 33380083 PMCID: PMC7771999 DOI: 10.1063/5.0035032] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 12/07/2020] [Indexed: 12/21/2022] Open
Abstract
Force fields for four small molecules, methane, ethane, methanol, and ethanol, were created by force matching MP2 gradients computed with triple-zeta-quality basis sets using the Adaptive Force Matching method. Without fitting to any experimental properties, the force fields created were able to predict hydration free energies, enthalpies of hydration, and diffusion constants in excellent agreements with experiments. The root mean square error for the predicted hydration free energies is within 1 kJ/mol of experimental measurements of Ben-Naim et al. [J. Chem. Phys. 81(4), 2016-2027 (1984)]. The good prediction of hydration free energies is particularly noteworthy, as it is an important fundamental property. Similar hydration free energies of ethane relative to methane and of ethanol relative to methanol are attributed to a near cancellation of cavitation penalty and favorable contributions from dispersion and Coulombic interactions as a result of the additional methyl group.
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Affiliation(s)
- T. Ryan Rogers
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, USA
| | - Feng Wang
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, USA
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Wan S, Bhati AP, Zasada SJ, Coveney PV. Rapid, accurate, precise and reproducible ligand-protein binding free energy prediction. Interface Focus 2020; 10:20200007. [PMID: 33178418 PMCID: PMC7653346 DOI: 10.1098/rsfs.2020.0007] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/11/2020] [Indexed: 02/06/2023] Open
Abstract
A central quantity of interest in molecular biology and medicine is the free energy of binding of a molecule to a target biomacromolecule. Until recently, the accurate prediction of binding affinity had been widely regarded as out of reach of theoretical methods owing to the lack of reproducibility of the available methods, not to mention their complexity, computational cost and time-consuming procedures. The lack of reproducibility stems primarily from the chaotic nature of classical molecular dynamics (MD) and the associated extreme sensitivity of trajectories to their initial conditions. Here, we review computational approaches for both relative and absolute binding free energy calculations, and illustrate their application to a diverse set of ligands bound to a range of proteins with immediate relevance in a number of medical domains. We focus on ensemble-based methods which are essential in order to compute statistically robust results, including two we have recently developed, namely thermodynamic integration with enhanced sampling and enhanced sampling of MD with an approximation of continuum solvent. Together, these form a set of rapid, accurate, precise and reproducible free energy methods. They can be used in real-world problems such as hit-to-lead and lead optimization stages in drug discovery, and in personalized medicine. These applications show that individual binding affinities equipped with uncertainty quantification may be computed in a few hours on a massive scale given access to suitable high-end computing resources and workflow automation. A high level of accuracy can be achieved using these approaches.
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Affiliation(s)
- Shunzhou Wan
- Centre for Computational Science, Department of Chemistry, University College London, London WC1H 0AJ, UK
| | - Agastya P. Bhati
- Centre for Computational Science, Department of Chemistry, University College London, London WC1H 0AJ, UK
| | - Stefan J. Zasada
- Centre for Computational Science, Department of Chemistry, University College London, London WC1H 0AJ, UK
| | - Peter V. Coveney
- Centre for Computational Science, Department of Chemistry, University College London, London WC1H 0AJ, UK
- Computational Science Laboratory, Institute for Informatics, Faculty of Science, University of Amsterdam, 1098XH Amsterdam, The Netherlands
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Oliveira MP, Andrey M, Rieder SR, Kern L, Hahn DF, Riniker S, Horta BAC, Hünenberger PH. Systematic Optimization of a Fragment-Based Force Field against Experimental Pure-Liquid Properties Considering Large Compound Families: Application to Saturated Haloalkanes. J Chem Theory Comput 2020; 16:7525-7555. [DOI: 10.1021/acs.jctc.0c00683] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Marina P. Oliveira
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Maurice Andrey
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Salomé R. Rieder
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Leyla Kern
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - David F. Hahn
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Sereina Riniker
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Bruno A. C. Horta
- Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-909, Brazil
| | - Philippe H. Hünenberger
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
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41
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Kashefolgheta S, Oliveira MP, Rieder SR, Horta BAC, Acree WE, Hünenberger PH. Evaluating Classical Force Fields against Experimental Cross-Solvation Free Energies. J Chem Theory Comput 2020; 16:7556-7580. [DOI: 10.1021/acs.jctc.0c00688] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Sadra Kashefolgheta
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Marina P. Oliveira
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Salomé R. Rieder
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Bruno A. C. Horta
- Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-909, Brazil
| | - William E. Acree
- Department of Chemistry, University of North Texas, 1155 Union Circle Drive #305070, Denton, Texas 76203, United States
| | - Philippe H. Hünenberger
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
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42
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Kabedev A, Hossain S, Hubert M, Larsson P, Bergström CAS. Molecular Dynamics Simulations Reveal Membrane Interactions for Poorly Water-Soluble Drugs: Impact of Bile Solubilization and Drug Aggregation. J Pharm Sci 2020; 110:176-185. [PMID: 33152373 DOI: 10.1016/j.xphs.2020.10.061] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/14/2020] [Accepted: 10/28/2020] [Indexed: 01/19/2023]
Abstract
Molecular transport mechanisms of poorly soluble hydrophobic drug compounds to lipid membranes were investigated using molecular dynamics (MD) simulations. The model compound danazol was used to investigate the mechanism(s) by which bile micelles delivered it to the membrane. The interactions between lipid membrane and pure drug aggregates-in the form of amorphous aggregates and nanocrystals-were also studied. Our simulations indicate that bile micelles formed in the intestinal fluid may facilitate danazol incorporation into cellular membranes through two different mechanisms. The micelle may be acting as: i) a shuttle that presents the danazol directly to the membrane or ii) an elevator that moves the solubilized danazol with it as the colloidal structure itself becomes incorporated and solubilized within the membrane. The elevator hypothesis was supported by complementary lipid monolayer adsorption experiments. In these experiments, colloidal structures formed with simulated intestinal fluid were observed to rapidly incorporate into the monolayer. Simulations of membrane interaction with drug aggregates showed that both the amorphous aggregates and crystalline nanostructures incorporated into the membrane. However, the amorphous aggregates solubilized more quickly than the nanocrystals into the membrane, thereby improving the danazol absorption.
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Affiliation(s)
- Aleksei Kabedev
- Department of Pharmacy, Uppsala University, Husargatan 3, 751 23 Uppsala, Sweden
| | - Shakhawath Hossain
- Department of Pharmacy, Uppsala University, Husargatan 3, 751 23 Uppsala, Sweden
| | - Madlen Hubert
- Department of Pharmacy, Uppsala University, Husargatan 3, 751 23 Uppsala, Sweden
| | - Per Larsson
- Department of Pharmacy, Uppsala University, Husargatan 3, 751 23 Uppsala, Sweden; The Swedish Drug Delivery Center (SweDeliver), Uppsala University, Husargatan 3, 751 23 Uppsala, Sweden
| | - Christel A S Bergström
- Department of Pharmacy, Uppsala University, Husargatan 3, 751 23 Uppsala, Sweden; The Swedish Drug Delivery Center (SweDeliver), Uppsala University, Husargatan 3, 751 23 Uppsala, Sweden.
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43
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He X, Man VH, Yang W, Lee TS, Wang J. A fast and high-quality charge model for the next generation general AMBER force field. J Chem Phys 2020; 153:114502. [PMID: 32962378 DOI: 10.1063/5.0019056] [Citation(s) in RCA: 238] [Impact Index Per Article: 59.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The General AMBER Force Field (GAFF) has been broadly used by researchers all over the world to perform in silico simulations and modelings on diverse scientific topics, especially in the field of computer-aided drug design whose primary task is to accurately predict the affinity and selectivity of receptor-ligand binding. The atomic partial charges in GAFF and the second generation of GAFF (GAFF2) were originally developed with the quantum mechanics derived restrained electrostatic potential charge, but in practice, users usually adopt an efficient charge method, Austin Model 1-bond charge corrections (AM1-BCC), based on which, without expensive ab initio calculations, the atomic charges could be efficiently and conveniently obtained with the ANTECHAMBER module implemented in the AMBER software package. In this work, we developed a new set of BCC parameters specifically for GAFF2 using 442 neutral organic solutes covering diverse functional groups in aqueous solution. Compared to the original BCC parameter set, the new parameter set significantly reduced the mean unsigned error (MUE) of hydration free energies from 1.03 kcal/mol to 0.37 kcal/mol. More excitingly, this new AM1-BCC model also showed excellent performance in the solvation free energy (SFE) calculation on diverse solutes in various organic solvents across a range of different dielectric constants. In this large-scale test with totally 895 neutral organic solvent-solute systems, the new parameter set led to accurate SFE predictions with the MUE and the root-mean-square-error of 0.51 kcal/mol and 0.65 kcal/mol, respectively. This newly developed charge model, ABCG2, paved a promising path for the next generation GAFF development.
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Affiliation(s)
- Xibing He
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
| | - Viet H Man
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
| | - Wei Yang
- Department of Chemistry and Biochemistry and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA
| | - Tai-Sung Lee
- Laboratory for Biomolecular Simulation Research, Center for Integrative Proteomics Research, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Junmei Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
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44
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Song LF, Merz KM. Evolution of Alchemical Free Energy Methods in Drug Discovery. J Chem Inf Model 2020; 60:5308-5318. [DOI: 10.1021/acs.jcim.0c00547] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Lin Frank Song
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, United States
| | - Kenneth M. Merz
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, United States
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Larsson P, Kneiszl RC, Marklund EG. MkVsites: A tool for creating GROMACS virtual sites parameters to increase performance in all-atom molecular dynamics simulations. J Comput Chem 2020; 41:1564-1569. [PMID: 32282082 PMCID: PMC7384070 DOI: 10.1002/jcc.26198] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/11/2020] [Accepted: 03/14/2020] [Indexed: 11/06/2022]
Abstract
The absolute performance of any all-atom molecular dynamics simulation is typically limited by the length of the individual timesteps taken when integrating the equations of motion. In the GROMACS simulation software, it has for a long time been possible to use so-called virtual sites to increase the length of the timestep, resulting in a large gain of simulation efficiency. Up until now, support for this approach has in practice been limited to the standard 20 amino acids however, shrinking the applicability domain of virtual sites. MkVsites is a set of python tools which provides a convenient way to obtain all parameters necessary to use virtual sites for virtually any molecules in a simulation. Required as input to MkVsites is the molecular topology of the molecule(s) in question, along with a specification of where to find the parent force field. As such, MkVsites can be a very valuable tool suite for anyone who is routinely using GROMACS for the simulation of molecular systems.
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Affiliation(s)
- Per Larsson
- Department of Pharmacy, Uppsala Biomedical Research Centre, Uppsala University, Uppsala, Sweden
| | - Rosita C Kneiszl
- Department of Pharmacy, Uppsala Biomedical Research Centre, Uppsala University, Uppsala, Sweden
| | - Erik G Marklund
- Department of Chemistry - BMC, Uppsala Biomedical Research Centre, Uppsala University, Uppsala, Sweden
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Fan S, Iorga BI, Beckstein O. Prediction of octanol-water partition coefficients for the SAMPL6-[Formula: see text] molecules using molecular dynamics simulations with OPLS-AA, AMBER and CHARMM force fields. J Comput Aided Mol Des 2020; 34:543-560. [PMID: 31960254 PMCID: PMC7667952 DOI: 10.1007/s10822-019-00267-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 11/27/2019] [Indexed: 10/25/2022]
Abstract
All-atom molecular dynamics simulations with stratified alchemical free energy calculations were used to predict the octanol-water partition coefficient [Formula: see text] of eleven small molecules as part of the SAMPL6-[Formula: see text] blind prediction challenge using four different force field parametrizations: standard OPLS-AA with transferable charges, OPLS-AA with non-transferable CM1A charges, AMBER/GAFF, and CHARMM/CGenFF. Octanol parameters for OPLS-AA, GAFF and CHARMM were validated by comparing the density as a function of temperature, the chemical potential, and the hydration free energy to experimental values. The partition coefficients were calculated from the solvation free energy for the compounds in water and pure ("dry") octanol or "wet" octanol with 27 mol% water dissolved. Absolute solvation free energies were computed by thermodynamic integration (TI) and the multistate Bennett acceptance ratio with uncorrelated samples from data generated by an established protocol using 5-ns windowed alchemical free energy perturbation (FEP) calculations with the Gromacs molecular dynamics package. Equilibration of sets of FEP simulations was quantified by a new measure of convergence based on the analysis of forward and time-reversed trajectories. The accuracy of the [Formula: see text] predictions was assessed by descriptive statistical measures such as the root mean square error (RMSE) of the data set compared to the experimental values. Discarding the first 1 ns of each 5-ns window as an equilibration phase had a large effect on the GAFF data, where it improved the RMSE by up to 0.8 log units, while the effect for other data sets was smaller or marginally worsened the agreement. Overall, CGenFF gave the best prediction with RMSE 1.2 log units, although for only eight molecules because the current CGenFF workflow for Gromacs does not generate files for certain halogen-containing compounds. Over all eleven compounds, GAFF gave an RMSE of 1.5. The effect of using a mixed water/octanol solvent slightly decreased the accuracy for CGenFF and GAFF and slightly increased it for OPLS-AA. The GAFF and OPLS-AA results displayed a systematic error where molecules were too hydrophobic whereas CGenFF appeared to be more balanced, at least on this small data set.
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Affiliation(s)
- Shujie Fan
- Department of Physics, Arizona State University, P.O. Box 871504, Tempe, AZ 85287-1504, USA
| | - Bogdan I Iorga
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, Labex LERMIT, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Oliver Beckstein
- Department of Physics and Center for Biological Physics, Arizona State University, P.O. Box 871504, Tempe, AZ 85287-1504, USA
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Shiref H, Bergman S, Clivio S, Sahai MA. The fine art of preparing membrane transport proteins for biomolecular simulations: Concepts and practical considerations. Methods 2020; 185:3-14. [PMID: 32081744 PMCID: PMC10062712 DOI: 10.1016/j.ymeth.2020.02.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 02/14/2020] [Accepted: 02/14/2020] [Indexed: 10/25/2022] Open
Abstract
Molecular dynamics (MD) simulations have developed into an invaluable tool in bimolecular research, due to the capability of the method in capturing molecular events and structural transitions that describe the function as well as the physiochemical properties of biomolecular systems. Due to the progressive development of more efficient algorithms, expansion of the available computational resources, as well as the emergence of more advanced methodologies, the scope of computational studies has increased vastly over time. We now have access to a multitude of online databases, software packages, larger molecular systems and novel ligands due to the phenomenon of emerging novel psychoactive substances (NPS). With so many advances in the field, it is understandable that novices will no doubt find it challenging setting up a protein-ligand system even before they run their first MD simulation. These initial steps, such as homology modelling, ligand docking, parameterization, protein preparation and membrane setup have become a fundamental part of the drug discovery pipeline, and many areas of biomolecular sciences benefit from the applications provided by these technologies. However, there still remains no standard on their usage. Therefore, our aim within this review is to provide a clear overview of a variety of concepts and methodologies to consider, providing a workflow for a case study of a membrane transport protein, the full-length human dopamine transporter (hDAT) in complex with different stimulants, where MD simulations have recently been applied successfully.
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Affiliation(s)
- Hana Shiref
- Department of Life Sciences, University of Roehampton, London SW15 4JD, UK
| | - Shana Bergman
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University (WCMC), New York, NY 10065, USA
| | | | - Michelle A Sahai
- Department of Life Sciences, University of Roehampton, London SW15 4JD, UK.
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Ayanlaja AA, Ji G, Wang J, Gao Y, Cheng B, Kanwore K, Zhang L, Xiong Y, Kambey PA, Gao D. Doublecortin undergo nucleocytoplasmic transport via the RanGTPase signaling to promote glioma progression. Cell Commun Signal 2020; 18:24. [PMID: 32050972 PMCID: PMC7017634 DOI: 10.1186/s12964-019-0485-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 11/20/2019] [Indexed: 12/13/2022] Open
Abstract
Background Nuclear translocation of several oncogenic proteins have previously been reported, but neither the translocation of doublecortin (DCX) nor the mechanism involved has been studied. DCX is a neuronal microtubule-associated protein (MAP) that is crucial for adult neurogenesis and neuronal migration and has been associated with poor prognosis in gliomas. Methods We probed DCX expression in different grades of glioma tissues and conventional cells via western blotting. Then we analyzed the expression pattern in the Oncomine cancer profiling database. Confocal Immunofluorescence was used to detect DCX expression in the cellular compartments, while subcellular fractionation was probed via western blotting. Pulse shape height analysis was utilized to verify DCX localization in a larger population of cells. Co-immunoprecipitation was used in detecting DCX-import receptors interactions. To probe for DCX functions, stable cells expressing high DCX expression or knockdown were generated using CRISPR-Cas9 viral transfection, while plasmid site-directed mutant constructs were used to validate putative nuclear localization sequence (NLS) predicted via conventional algorithms and comparison with classical NLSs. in-silico modeling was performed to validate DCX interactions with import receptors via the selected putative NLS. Effects of DCX high expression, knockdown, mutation, and/or deletion of putative NLS sites were probed via Boyden’s invasion assay and wound healing migration assays, and viability was detected by CCK8 assays in-vitro, while xenograft tumor model was performed in nude mice. Results DCX undergoes nucleocytoplasmic movement via the RanGTPase signaling pathway with an NLS located on the N-terminus between serine47-tyrosine70. This translocation could be stimulated by MARK’s phosphorylation of the serine 47 residue flanking the NLS due to aberrant expression of glial cell line-derived neurotrophic factor (GDNF). High expression and nuclear accumulation of DCX improve invasive glioma abilities in-vitro and in-vivo. Moreover, knocking down or blocking DCX nuclear import attenuates invasiveness and proliferation of glioma cells. Conclusion Collectively, this study highlights a remarkable phenomenon in glioma, hence revealing potential glioma dependencies on DCX expression, which is amenable to targeted therapy. Video abstract
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Affiliation(s)
- Abiola Abdulrahman Ayanlaja
- Department of Neurobiology and Anatomy, Key Laboratory of Neurobiology, Xuzhou Medical University, 209, Tongshan Road, Xuzhou, 221004, China
| | - Guanquan Ji
- Department of Neurobiology and Anatomy, Key Laboratory of Neurobiology, Xuzhou Medical University, 209, Tongshan Road, Xuzhou, 221004, China.,Department of Neurosurgery, The Second Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China.,Department of Neurosurgery, The Third Affiliated Hospital of Henan University of Science and Technology, Henan, China
| | - Jie Wang
- Department of Neurobiology and Anatomy, Key Laboratory of Neurobiology, Xuzhou Medical University, 209, Tongshan Road, Xuzhou, 221004, China
| | - Yue Gao
- Department of Neurobiology and Anatomy, Key Laboratory of Neurobiology, Xuzhou Medical University, 209, Tongshan Road, Xuzhou, 221004, China
| | - Bo Cheng
- Department of Neurobiology and Anatomy, Key Laboratory of Neurobiology, Xuzhou Medical University, 209, Tongshan Road, Xuzhou, 221004, China
| | - Kouminin Kanwore
- Department of Neurobiology and Anatomy, Key Laboratory of Neurobiology, Xuzhou Medical University, 209, Tongshan Road, Xuzhou, 221004, China
| | - Lin Zhang
- Department of Neurobiology and Anatomy, Key Laboratory of Neurobiology, Xuzhou Medical University, 209, Tongshan Road, Xuzhou, 221004, China
| | - Ye Xiong
- Department of Neurobiology and Anatomy, Key Laboratory of Neurobiology, Xuzhou Medical University, 209, Tongshan Road, Xuzhou, 221004, China
| | - Piniel Alphayo Kambey
- Department of Neurobiology and Anatomy, Key Laboratory of Neurobiology, Xuzhou Medical University, 209, Tongshan Road, Xuzhou, 221004, China
| | - Dianshuai Gao
- Department of Neurobiology and Anatomy, Key Laboratory of Neurobiology, Xuzhou Medical University, 209, Tongshan Road, Xuzhou, 221004, China.
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Muthoka RM, Kim HC, Kim JW, Zhai L, Panicker PS, Kim J. Steered Pull Simulation to Determine Nanomechanical Properties of Cellulose Nanofiber. MATERIALS 2020; 13:ma13030710. [PMID: 32033273 PMCID: PMC7041381 DOI: 10.3390/ma13030710] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 01/21/2020] [Accepted: 02/01/2020] [Indexed: 11/16/2022]
Abstract
Cellulose nanofiber (CNF) exhibits excellent mechanical properties, which has been extensively proven through experimental techniques. However, understanding the mechanisms and the inherent structural behavior of cellulose is important in its vastly growing research areas of applications. This study focuses on taking a look into what happens to the atomic molecular interactions of CNF, mainly hydrogen bond, in the presence of external force. This paper investigates the hydrogen bond disparity within CNF structure. To achieve this, molecular dynamics simulations of cellulose Iβ nanofibers are carried out in equilibrated conditions in water using GROMACS software in conjunction with OPLS-AA force field. It is noted that the hydrogen bonds within the CNF are disrupted when a pulling force is applied. The simulated Young’s modulus of CNF is found to be 161 GPa. A simulated shear within the cellulose chains presents a trend with more hydrogen bond disruptions at higher forces.
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Gapsys V, Pérez-Benito L, Aldeghi M, Seeliger D, van Vlijmen H, Tresadern G, de Groot BL. Large scale relative protein ligand binding affinities using non-equilibrium alchemy. Chem Sci 2019; 11:1140-1152. [PMID: 34084371 PMCID: PMC8145179 DOI: 10.1039/c9sc03754c] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 12/01/2019] [Indexed: 12/14/2022] Open
Abstract
Ligand binding affinity calculations based on molecular dynamics (MD) simulations and non-physical (alchemical) thermodynamic cycles have shown great promise for structure-based drug design. However, their broad uptake and impact is held back by the notoriously complex setup of the calculations. Only a few tools other than the free energy perturbation approach by Schrödinger Inc. (referred to as FEP+) currently enable end-to-end application. Here, we present for the first time an approach based on the open-source software pmx that allows to easily set up and run alchemical calculations for diverse sets of small molecules using the GROMACS MD engine. The method relies on theoretically rigorous non-equilibrium thermodynamic integration (TI) foundations, and its flexibility allows calculations with multiple force fields. In this study, results from the Amber and Charmm force fields were combined to yield a consensus outcome performing on par with the commercial FEP+ approach. A large dataset of 482 perturbations from 13 different protein-ligand datasets led to an average unsigned error (AUE) of 3.64 ± 0.14 kJ mol-1, equivalent to Schrödinger's FEP+ AUE of 3.66 ± 0.14 kJ mol-1. For the first time, a setup is presented for overall high precision and high accuracy relative protein-ligand alchemical free energy calculations based on open-source software.
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Affiliation(s)
- Vytautas Gapsys
- Computational Biomolecular Dynamics Group, Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry D-37077 Göttingen Germany
| | - Laura Pérez-Benito
- Computational Chemistry, Janssen Research & Development, Janssen Pharmaceutica N. V. Turnhoutseweg 30 B-2340 Beerse Belgium
| | - Matteo Aldeghi
- Computational Biomolecular Dynamics Group, Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry D-37077 Göttingen Germany
| | - Daniel Seeliger
- Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG Birkendorfer Strasse 65 D-88397 Biberach a.d. Riss Germany
| | - Herman van Vlijmen
- Computational Chemistry, Janssen Research & Development, Janssen Pharmaceutica N. V. Turnhoutseweg 30 B-2340 Beerse Belgium
| | - Gary Tresadern
- Computational Chemistry, Janssen Research & Development, Janssen Pharmaceutica N. V. Turnhoutseweg 30 B-2340 Beerse Belgium
| | - Bert L de Groot
- Computational Biomolecular Dynamics Group, Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry D-37077 Göttingen Germany
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