101
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Avallone N, Huppert S, Depondt P, Andriambariarijaona L, Datchi F, Ninet S, Plé T, Spezia R, Finocchi F. Orientational Disorder Drives Site Disorder in Plastic Ammonia Hemihydrate. PHYSICAL REVIEW LETTERS 2024; 133:106102. [PMID: 39303235 DOI: 10.1103/physrevlett.133.106102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 07/24/2024] [Indexed: 09/22/2024]
Abstract
In the 2-10 GPa pressure range, ammonia hemihydrate H_{2}O:(NH_{3})_{2} (AHH) is a molecular solid in which intermolecular interactions are ruled by distinct types of hydrogen bonds. Upon heating, the low-temperature ordered P2_{1}/c crystal (AHH-II) transits to a bcc phase (AHH-pbcc) where each site is randomly occupied by water or ammonia. In addition to the site disorder, experiments suggest that AHH-pbcc is a plastic solid, but the physical origin and mechanisms at play for the rotational and site disordering remain unknown. Using large-scale (∼10^{5} atoms) and long-time (>10 ns) simulations, we show that, as temperature rises above the transition line, orientational disorder sets in, breaking the strongest hydrogen bonds that provide the largest contribution to the cohesion of the ordered AHH-II phase and enabling the molecules to migrate from a crystal site to a neighboring one. This generates a plastic molecular alloy with site disorder while the solid state is overall maintained until melting at a higher temperature. The case of high (P,T) plastic ammonia hemihydrate can be extended to other water-ammonia alloys where a similar interplay between distinct hydrogen bonds occurs.
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102
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Chakraborty A, Ghosh R, Soumya Mohapatra S, Barik S, Biswas A, Chowdhuri S. Repurposing of antimycobacterium drugs for COVID-19 treatment by targeting SARS CoV-2 main protease: An in-silico perspective. Gene 2024; 922:148553. [PMID: 38734190 DOI: 10.1016/j.gene.2024.148553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 04/27/2024] [Accepted: 05/08/2024] [Indexed: 05/13/2024]
Abstract
The global mortality rate has been significantly impacted by the COVID-19 pandemic, caused by the SARS CoV-2 virus. Although the pursuit for a potent antiviral is still in progress, experimental therapies based on repurposing of existing drugs is being attempted. One important therapeutic target for COVID-19 is the main protease (Mpro) that cleaves the viral polyprotein in its replication process. Recently minocycline, an antimycobacterium drug, has been successfully implemented for the treatment of COVID-19 patients. But it's mode of action is still far from clear. Furthermore, it remains unresolved whether alternative antimycobacterium drugs can effectively regulate SARS CoV-2 by inhibiting the enzymatic activity of Mpro. To comprehend these facets, eight well-established antimycobacterium drugs were put through molecular docking experiments. Four of the antimycobacterium drugs (minocycline, rifampicin, clofazimine and ofloxacin) were selected by comparing their binding affinities towards Mpro. All of the four drugs interacted with both the catalytic residues of Mpro (His41 and Cys145). Additionally, molecular dynamics experiments demonstrated that the Mpro-minocyline complex has enhanced stability, experiences reduced conformational fluctuations and greater compactness than other three Mpro-antimycobacterium and Mpro-N3/lopinavir complexes. This research furnishes evidences for implementation of minocycline against SARS CoV-2. In addition, our findings also indicate other three antimycobacterium/antituberculosis drugs (rifampicin, clofazimine and ofloxacin) could potentially be evaluated for COVID-19 therapy.
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Affiliation(s)
- Ayon Chakraborty
- University Institute of Biotechnology, University Centre for Research & Development, Chandigarh University, Mohali, India
| | - Rajesh Ghosh
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | | | - Subhashree Barik
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | - Ashis Biswas
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India.
| | - Snehasis Chowdhuri
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India.
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103
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Kant R, Tilford H, Freitas CS, Ferreira DAS, Ng J, Rucinski G, Watkins J, Pemberton R, Abramyan TM, Contreras SC, Vera A, Christodoulides M. Antimicrobial activity of compounds identified by artificial intelligence discovery engine targeting enzymes involved in Neisseria gonorrhoeae peptidoglycan metabolism. Biol Res 2024; 57:62. [PMID: 39238057 PMCID: PMC11375863 DOI: 10.1186/s40659-024-00543-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 08/27/2024] [Indexed: 09/07/2024] Open
Abstract
BACKGROUND Neisseria gonorrhoeae (Ng) causes the sexually transmitted disease gonorrhoea. There are no vaccines and infections are treated principally with antibiotics. However, gonococci rapidly develop resistance to every antibiotic class used and there is a need for developing new antimicrobial treatments. In this study we focused on two gonococcal enzymes as potential antimicrobial targets, namely the serine protease L,D-carboxypeptidase LdcA (NgO1274/NEIS1546) and the lytic transglycosylase LtgD (NgO0626/NEIS1212). To identify compounds that could interact with these enzymes as potential antimicrobials, we used the AtomNet virtual high-throughput screening technology. We then did a computational modelling study to examine the interactions of the most bioactive compounds with their target enzymes. The identified compounds were tested against gonococci to determine minimum inhibitory and bactericidal concentrations (MIC/MBC), specificity, and compound toxicity in vitro. RESULTS AtomNet identified 74 compounds that could potentially interact with Ng-LdcA and 84 compounds that could potentially interact with Ng-LtgD. Through MIC and MBC assays, we selected the three best performing compounds for both enzymes. Compound 16 was the most active against Ng-LdcA, with a MIC50 value < 1.56 µM and MBC50/90 values between 0.195 and 0.39 µM. In general, the Ng-LdcA compounds showed higher activity than the compounds directed against Ng-LtgD, of which compound 45 had MIC50 values of 1.56-3.125 µM and MBC50/90 values between 3.125 and 6.25 µM. The compounds were specific for gonococci and did not kill other bacteria. They were also non-toxic for human conjunctival epithelial cells as judged by a resazurin assay. To support our biological data, in-depth computational modelling study detailed the interactions of the compounds with their target enzymes. Protein models were generated in silico and validated, the active binding sites and amino acids involved elucidated, and the interactions of the compounds interacting with the enzymes visualised through molecular docking and Molecular Dynamics Simulations for 50 ns and Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA). CONCLUSIONS We have identified bioactive compounds that appear to target the N. gonorrhoeae LdcA and LtgD enzymes. By using a reductionist approach involving biological and computational data, we propose that compound Ng-LdcA-16 and Ng-LtgD-45 are promising anti-gonococcal compounds for further development.
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Affiliation(s)
- Ravi Kant
- Neisseria Research Group, Molecular Microbiology, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, England, SO16 6YD
- Medical Biotechnology Laboratory, Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, North Campus, Delhi, 110007, India
| | - Hannah Tilford
- Neisseria Research Group, Molecular Microbiology, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, England, SO16 6YD
| | - Camila S Freitas
- Neisseria Research Group, Molecular Microbiology, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, England, SO16 6YD
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 30130-100, Brazil
| | - Dayana A Santos Ferreira
- Neisseria Research Group, Molecular Microbiology, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, England, SO16 6YD
- Laboratory of Pathophysiology, Butantan Institute, Av. Vital Brazil, 1500, São Paulo, SP, 05503-900, Brazil
| | - James Ng
- Neisseria Research Group, Molecular Microbiology, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, England, SO16 6YD
| | - Gwennan Rucinski
- Neisseria Research Group, Molecular Microbiology, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, England, SO16 6YD
| | - Joshua Watkins
- Neisseria Research Group, Molecular Microbiology, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, England, SO16 6YD
| | - Ryan Pemberton
- ATOMWISE, 717 Market Street, Suite 800, San Francisco, CA, 94103, USA
| | - Tigran M Abramyan
- ATOMWISE, 717 Market Street, Suite 800, San Francisco, CA, 94103, USA
| | | | - Alejandra Vera
- Laboratorio de Bacteriología, Escuela de Medicina, Universidad de Valparaíso, Valparaíso, Chile
| | - Myron Christodoulides
- Neisseria Research Group, Molecular Microbiology, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, England, SO16 6YD.
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104
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Costanzo A, Fata F, Freda I, De Sciscio ML, Gugole E, Bulfaro G, Di Renzo M, Barbizzi L, Exertier C, Parisi G, D'Abramo M, Vallone B, Savino C, Montemiglio LC. Binding of steroid substrates reveals the key to the productive transition of the cytochrome P450 OleP. Structure 2024; 32:1465-1476.e3. [PMID: 38971159 DOI: 10.1016/j.str.2024.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 05/08/2024] [Accepted: 06/11/2024] [Indexed: 07/08/2024]
Abstract
OleP is a bacterial cytochrome P450 involved in oleandomycin biosynthesis as it catalyzes regioselective epoxidation on macrolide intermediates. OleP has recently been reported to convert lithocholic acid (LCA) into murideoxycholic acid through a highly regioselective reaction and to unspecifically hydroxylate testosterone (TES). Since LCA and TES mainly differ by the substituent group at the C17, here we used X-ray crystallography, equilibrium binding assays, and molecular dynamics simulations to investigate the molecular basis of the diverse reactivity observed with the two steroids. We found that the differences in the structure of TES and LCA affect the capability of these molecules to directly form hydrogen bonds with N-terminal residues of OleP internal helix I. The establishment of these contacts, by promoting the bending of helix I, fosters an efficient trigger of the open-to-closed structural transition that occurs upon substrate binding to OleP and contributes to the selectivity of the subsequent monooxygenation reaction.
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Affiliation(s)
- Antonella Costanzo
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza, University of Rome, P. le Aldo Moro, 5, 00185 Rome, Italy; Takis Biotech, Via di Castel Romano 100, 00128 Rome, Italy
| | - Francesca Fata
- Institute of Molecular Biology and Pathology c/o Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza, University of Rome, National Research Council, P.le Aldo Moro, 5, 00185 Rome, Italy
| | - Ida Freda
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza, University of Rome, P. le Aldo Moro, 5, 00185 Rome, Italy
| | - Maria Laura De Sciscio
- Department of Chemistry, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy
| | - Elena Gugole
- Institute of Molecular Biology and Pathology c/o Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza, University of Rome, National Research Council, P.le Aldo Moro, 5, 00185 Rome, Italy
| | - Giovanni Bulfaro
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza, University of Rome, P. le Aldo Moro, 5, 00185 Rome, Italy; Takis Biotech, Via di Castel Romano 100, 00128 Rome, Italy
| | - Matteo Di Renzo
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza, University of Rome, P. le Aldo Moro, 5, 00185 Rome, Italy
| | - Luca Barbizzi
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza, University of Rome, P. le Aldo Moro, 5, 00185 Rome, Italy
| | - Cécile Exertier
- Institute of Molecular Biology and Pathology c/o Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza, University of Rome, National Research Council, P.le Aldo Moro, 5, 00185 Rome, Italy
| | - Giacomo Parisi
- Department of Basic and Applied Sciences for Engineering (SBAI), Sapienza, University of Rome, Via Antonio Scarpa, 16, 00161 Rome, Italy
| | - Marco D'Abramo
- Department of Chemistry, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy
| | - Beatrice Vallone
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza, University of Rome, P. le Aldo Moro, 5, 00185 Rome, Italy; Institute of Molecular Biology and Pathology c/o Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza, University of Rome, National Research Council, P.le Aldo Moro, 5, 00185 Rome, Italy.
| | - Carmelinda Savino
- Institute of Molecular Biology and Pathology c/o Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza, University of Rome, National Research Council, P.le Aldo Moro, 5, 00185 Rome, Italy.
| | - Linda Celeste Montemiglio
- Institute of Molecular Biology and Pathology c/o Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza, University of Rome, National Research Council, P.le Aldo Moro, 5, 00185 Rome, Italy.
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105
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Baumann HM, Mobley DL. Impact of protein conformations on binding free energy calculations in the beta-secretase 1 system. J Comput Chem 2024; 45:2024-2033. [PMID: 38725239 PMCID: PMC11236511 DOI: 10.1002/jcc.27365] [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: 09/12/2023] [Revised: 01/13/2024] [Accepted: 03/24/2024] [Indexed: 07/11/2024]
Abstract
In binding free energy calculations, simulations must sample all relevant conformations of the system in order to obtain unbiased results. For instance, different ligands can bind to different metastable states of a protein, and if these protein conformational changes are not sampled in relative binding free energy calculations, the contribution of these states to binding is not accounted for and thus calculated binding free energies are inaccurate. In this work, we investigate the impact of different beta-sectretase 1 (BACE1) protein conformations obtained from x-ray crystallography on the binding of BACE1 inhibitors. We highlight how these conformational changes are not adequately sampled in typical molecular dynamics simulations. Furthermore, we show that insufficient sampling of relevant conformations induces substantial error in relative binding free energy calculations, as judged by a variation in calculated relative binding free energies up to 2 kcal/mol depending on the starting protein conformation. These results emphasize the importance of protein conformational sampling and pose this BACE1 system as a challenge case for further method development in the area of enhanced protein conformational sampling, either in combination with binding calculations or as an endpoint correction.
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Affiliation(s)
- Hannah M Baumann
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California, USA
| | - David L Mobley
- Department of Chemistry, University of California, Irvine, California, USA
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106
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Kumari S, Vijaykumar S, Kumar V, Ranjan R, Alti D, Singh V, Ahmed G, Sahoo GC, Pandey K, Kumar A. In silico and in vitro evaluation of the immunogenic potential of Leishmania donovani ascorbate peroxidase and its derived peptides. Acta Trop 2024:107381. [PMID: 39244139 DOI: 10.1016/j.actatropica.2024.107381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 08/13/2024] [Accepted: 09/04/2024] [Indexed: 09/09/2024]
Abstract
The control and eradication of any infectious disease is only possible with a potential vaccine, which has not been accomplished for human visceral leishmaniasis (VL). The lack of vaccines may increase the risk of VL outbreaks periodically in endemic zones. Identifying a reliable vaccine candidate for Leishmania is a major challenge. Here, we considered Leishmania donovani ascorbate peroxidase (LdAPx) for its in vitro evaluation with the hope of future vaccine candidates for VL. LdAPx was selected based on its unique presence in Leishmania and virulence in VL pathogenesis. Initially, we found antibodies against recombinant LdAPx (rLdAPx) in the serum of VL patients. Therefore, using bioinformatics, we predicted and selected ten (MHC class I and II) peptides. These peptides, evaluated in vitro with PBMCs from healthy, active VL, and treated VL individuals induced PBMC proliferation, IFN-γ secretion, and Nitric Oxide (NO) production, indicating host-protective immune responses. Among them, three peptides (PEP6, PEP8, and PEP9) consistently elicited a Th1-type immune response in PBMCs. Treated VL individuals showed a stronger Th1 response compared to active VL patients and healthy subjects, highlighting these peptides' potential as vaccine candidates. Further studies are on the way toward evaluating the LdAPx-derived peptides or sub-unit vaccine in animal models against the L. donovani challenge.
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Affiliation(s)
- Shobha Kumari
- Department of Biochemistry, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna, 800007, Bihar, India
| | - Saravanan Vijaykumar
- Statistics/Bioinformatics, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna, 800007, Bihar, India; National Center for Diseases Informatics and Research, Bengaluru, 562110, Karnataka, India
| | - Vikash Kumar
- Department of Biochemistry, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna, 800007, Bihar, India
| | - Ravi Ranjan
- Department of Biochemistry, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna, 800007, Bihar, India
| | - Dayakar Alti
- Department of Immunology, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna, 800007, Bihar, India
| | - Veer Singh
- Department of Biochemistry, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna, 800007, Bihar, India
| | - Ghufran Ahmed
- Department of Biochemistry, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna, 800007, Bihar, India
| | - Ganesh Chandra Sahoo
- Department of Virology, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna, 800007, Bihar, India
| | - Krishna Pandey
- Department of Clinical Medicine, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna, 800007, Bihar, India
| | - Ashish Kumar
- Department of Biochemistry, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna, 800007, Bihar, India.
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107
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Das G, Harikrishna S, Gore KR. Investigating the Effect of Chemical Modifications on the Ribose Sugar Conformation, Watson-Crick Base Pairing, and Intrastrand Stacking Interactions: A Theoretical Approach. J Phys Chem B 2024; 128:8313-8331. [PMID: 39172066 DOI: 10.1021/acs.jpcb.4c02557] [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: 08/23/2024]
Abstract
Over the last few decades, chemically modified sugars have been incorporated into nucleic acid-based therapeutics to improve their pharmacological potential. Chemical modification can influence the sugar conformation, Watson-Crick hydrogen (W-C) bonding, and nucleobase stacking interactions, which play major roles in the structural integrity and dynamic properties of nucleic acid duplexes. In this study, we categorized 33 uridine (U*) and cytidine (C*) sugar modifications and calculated their sugar conformational parameters. We also calculated the Watson-Crick hydrogen bond energies of the modified RNA-type base pairs (U*:A and C*:G) using DFT and sSAPT0 methods. The W-C base pairing energy calculations suggested that the South-type modified sugar strengthens the C*:G base pair and weakens the U*:A base pair compared to the unmodified one. In contrast, the North-type sugar modifications form weaker C*:G base pair and marginally stronger U*:A base pair compared to the South-type modified sugars. Moreover, intrastrand base stacking energies were calculated for 15 modifications incorporated at the fourth position in 7-mer non-self-complementary RNA duplexes [(GCAU*GAC)2 and (GCAC*GAC)2], utilizing molecular dynamics simulation and quantum mechanical (DFT and sSAPT0) methods. The sugar modifications were found to have minimal effect on the intrastrand base-stacking interactions. However, the glycol nucleic acid modification disturbs the intrastrand base-stacking significantly, corroborating the experimental data.
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Affiliation(s)
- Gourav Das
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
| | - S Harikrishna
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Kiran R Gore
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
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108
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Vicars Z, Choi J, Marks SM, Remsing RC, Patel AJ. Interfacial Ice Density Fluctuations Inform Surface Ice-Philicity. J Phys Chem B 2024; 128:8512-8521. [PMID: 39171456 DOI: 10.1021/acs.jpcb.4c03783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
The propensity of a surface to nucleate ice or bind to ice is governed by its ice-philicity─its relative preference for ice over liquid water. However, the relationship between the features of a surface and its ice-philicity is not well understood, and for surfaces with chemical or topographical heterogeneity, such as proteins, their ice-philicity is not even well-defined. In the analogous problem of surface hydrophobicity, it has been shown that hydrophobic surfaces display enhanced low water-density (vapor-like) fluctuations in their vicinity. To interrogate whether enhanced ice-like fluctuations are similarly observed near ice-philic surfaces, here we use molecular simulations and enhanced sampling techniques. Using a family of model surfaces for which the wetting coefficient, k, has previously been characterized, we show that the free energy of observing rare interfacial ice-density fluctuations decreases monotonically with increasing k. By utilizing this connection, we investigate a set of fcc systems and find that the (110) surface is more ice-philic than the (111) or (100) surfaces. By additionally analyzing the structure of interfacial ice, we find that all surfaces prefer to bind to the basal plane of ice, and the topographical complementarity of the (110) surface to the basal plane explains its higher ice-philicity. Using enhanced interfacial ice-like fluctuations as a measure of surface ice-philicity, we then characterize the ice-philicity of chemically heterogeneous and topologically complex systems. In particular, we study the spruce budworm antifreeze protein (sbwAFP), which binds to ice using a known ice-binding site (IBS) and resists engulfment using nonbinding sites of the protein (NBSs). We find that the IBS displays enhanced interfacial ice-density fluctuations and is therefore more ice-philic than the two NBSs studied. We also find the two NBSs are similarly ice-phobic. By establishing a connection between interfacial ice-like fluctuations and surface ice-philicity, our findings thus provide a way to characterize the ice-philicity of heterogeneous surfaces.
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Affiliation(s)
- Zachariah Vicars
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Jeongmoon Choi
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Sean M Marks
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Richard C Remsing
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Amish J Patel
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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109
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Dabas A, Goyal B. Structural Reorganization Mechanism of the Aβ 42 Fibril Mediated by N-Substituted Oligopyrrolamide ADH-353. ACS Chem Neurosci 2024; 15:3136-3151. [PMID: 39158263 DOI: 10.1021/acschemneuro.4c00253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/20/2024] Open
Abstract
The inhibition of amyloid-β (Aβ) fibrillation and clearance of Aβ aggregates have emerged as a potential pharmacological strategy to alleviate Aβ aggregate-induced neurotoxicity in Alzheimer's disease (AD). Maity et al. shortlisted ADH-353 from a small library of positively charged N-substituted oligopyrrolamides for its notable ability to inhibit Aβ fibrillation, disintegrate intracellular cytotoxic Aβ oligomers, and alleviate Aβ-induced cytotoxicity in the SH-SY5Y and N2a cells. However, the molecular mechanism through which ADH-353 interacts with the Aβ42 fibrils, leading to their disruption and subsequent clearance, remains unclear. Thus, a detailed molecular mechanism underlying the disruption of neurotoxic Aβ42 fibrils (PDB ID 2NAO) by ADH-353 has been illuminated in this work using molecular dynamics simulations. Interestingly, conformational snapshots during simulation depicted the shortening and disappearance of β-strands and the emergence of a helix conformation, indicating a loss of the well-organized β-sheet-rich structure of the disease-relevant Aβ42 fibril on the incorporation of ADH-353. ADH-353 binds strongly to the Aβ42 fibril (ΔGbinding= -142.91 ± 1.61 kcal/mol) with a notable contribution from the electrostatic interactions between positively charged N-propylamine side chains of ADH-353 with the glutamic (Glu3, Glu11, and Glu22) and aspartic (Asp7 and Asp23) acid residues of the Aβ42 fibril. This aligns well with heteronuclear single quantum coherence NMR studies, which depict that the binding of ADH-353 with the Aβ peptide is driven by electrostatic and hydrophobic contacts. Furthermore, a noteworthy decrease in the binding affinity of Aβ42 fibril chains on the incorporation of ADH-353 indicates the weakening of interchain interactions leading to the disruption of the double-horseshoe conformation of the Aβ42 fibril. The illumination of key interactions responsible for the destabilization of the Aβ42 fibril by ADH-353 in this work will greatly aid in designing new chemical scaffolds with enhanced efficacy for the clearance of Aβ aggregates in AD.
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Affiliation(s)
- Arushi Dabas
- Department of Chemistry & Biochemistry, Thapar Institute of Engineering & Technology, Patiala, Punjab 147004, India
| | - Bhupesh Goyal
- Department of Chemistry & Biochemistry, Thapar Institute of Engineering & Technology, Patiala, Punjab 147004, India
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110
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Zhang J, Fan X, Wang P, Liang R, Wang D, Xu J, Zhang D, Xie Y, Liao Q, Jiao Z, Shi Y, Peng G. Identification of novel broad-spectrum antiviral drugs targeting the N-terminal domain of the FIPV nucleocapsid protein. Int J Biol Macromol 2024; 279:135352. [PMID: 39242012 DOI: 10.1016/j.ijbiomac.2024.135352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 08/25/2024] [Accepted: 09/03/2024] [Indexed: 09/09/2024]
Abstract
Coronaviruses pose serious threats to human and animal health worldwide, of which their structural nucleocapsid (N) proteins play multiple key roles in viral replication. However, the structures of animal coronavirus N proteins are poorly understood, posing challenges for research on their functions and pathogenic mechanisms as well as the development of N protein-based antiviral drugs. Therefore, N proteins must be further explored as potential antiviral targets. We determined the structure of the NNTD of feline infectious peritonitis virus (FIPV) and identified 3,6-dihydroxyflavone (3,6- DHF) as an effective N protein inhibitor. 3,6-DHF successfully inhibited FIPV replication in CRFK cells, showing broad-spectrum activity and effectiveness against drugresistant strains. Our study provides important insights for developing novel broadspectrum anti-coronavirus drugs and treating infections caused by drug-resistant mutant strains.
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Affiliation(s)
- Jintao Zhang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China; Hongshan Laboratory, Wuhan, China
| | - Xinyu Fan
- Department of Biotechnology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Pengpeng Wang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China; Hongshan Laboratory, Wuhan, China
| | - Rui Liang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China; Hongshan Laboratory, Wuhan, China
| | - Donghan Wang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China; Hongshan Laboratory, Wuhan, China
| | - Juan Xu
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China; Hongshan Laboratory, Wuhan, China
| | - Ding Zhang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China; Hongshan Laboratory, Wuhan, China
| | - Yunfei Xie
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China; Hongshan Laboratory, Wuhan, China
| | - Qi Liao
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China; Hongshan Laboratory, Wuhan, China
| | - Zhe Jiao
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China; Hongshan Laboratory, Wuhan, China.
| | - Yuejun Shi
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China; Hongshan Laboratory, Wuhan, China.
| | - Guiqing Peng
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China; Hongshan Laboratory, Wuhan, China.
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111
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Devi M, Paul S. Comprehending the Efficacy of Whitlock's Caffeine-Pincered Molecular Tweezer on β-Amyloid Aggregation. ACS Chem Neurosci 2024; 15:3202-3219. [PMID: 39126645 DOI: 10.1021/acschemneuro.4c00387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2024] Open
Abstract
Alzheimer's disease (AD) stands as one of the most prevalent neurodegenerative conditions, leading to cognitive impairment, with no cure and preventive measures. Misfolding and aberrant aggregation of amyloid-β (Aβ) peptides are believed to be the underlying cause of AD. These amyloid aggregates culminate in the development of toxic Aβ oligomers and subsequent accumulation of β-amyloid plaques amidst neuronal cells in the brain, marking the hallmarks of AD. Drug development for the potentially curative treatment of Alzheimer's is, therefore, a tremendous challenge for the scientific community. In this study, we investigate the potency of Whitlock's caffeine-armed molecular tweezer in combating the deleterious effects of Aβ aggregation, with special emphasis on the seven residue Aβ16-22 fragment. Extensive all-atom molecular dynamics simulations are conducted to probe the various structural and conformational transitions of the peptides in an aqueous medium in both the presence and absence of tweezers. To explore the specifics of peptide-tweezer interactions, radial distribution functions, contact number calculations, binding free energies, and 2-D kernel density plots depicting the variation of distance-angle between the aromatic planes of the peptide-tweezer pair are computed. The central hydrophobic core, particularly the aromatic Phe residues, is crucial in the development of harmful amyloid oligomers. Notably, all analyses indicate reduced interpeptide interactions in the presence of the tweezer, which is attributed to the tweezer-Phe aromatic interaction. Upon increasing the tweezer concentration, the residues of the peptide are further encased in a hydrophobic environment created by the self-aggregating tweezer cluster, leading to the segregation of the peptide residues. This is further aided by the weakening of interstrand hydrogen bonding between the peptides, thereby impeding their self-aggregation and preventing the formation of neurotoxic β-amyloid. Furthermore, the study also highlights the efficacy of the molecular tweezer in destabilizing preformed amyloid fibrils as well as hindering the aggregation of the full-length Aβ1-42 peptide.
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Affiliation(s)
- Madhusmita Devi
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India
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112
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Larocca M, Floresta G, Verderese D, Cilibrizzi A. Dominant Chemical Interactions Governing the Folding Mechanism of Oligopeptides. Int J Mol Sci 2024; 25:9586. [PMID: 39273531 PMCID: PMC11395422 DOI: 10.3390/ijms25179586] [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: 08/06/2024] [Revised: 08/29/2024] [Accepted: 09/03/2024] [Indexed: 09/15/2024] Open
Abstract
The hydrophobic effect is the main factor that drives the folding of polypeptide chains. In this study, we have examined the influence of the hydrophobic effect in the context of the main mechanical forces approach, mainly in relation to the establishment of specific interplays, such as hydrophobic and CH-π cloud interactions. By adopting three oligopeptides as model systems to assess folding features, we demonstrate herein that these finely tuned interactions dominate over electrostatic interactions, including H-bonds and electrostatic attractions/repulsions. The folding mechanism analysed here demonstrates cooperation at the single-residue level, for which we propose the terminology of "single residues cooperative folding". Overall, hydrophobic and CH-π cloud interactions produce the main output of the hydrophobic effect and govern the folding mechanism, as demonstrated in this study with small polypeptide chains, which in turn represent the main secondary structures in proteins.
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Affiliation(s)
- Michele Larocca
- Istituto di Metodologie per l'Analisi Ambientale-Consiglio Nazionale delle Ricerche (CNR-IMAA), Contrada, Santa. Loja, 85050 Potenza, Italy
| | - Giuseppe Floresta
- Department of Drug and Health Sciences, University of Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Daniele Verderese
- Dipartimento di Scienze Economiche e Statistiche, Università di Salerno, via Giovanni Paolo II, 132, 84084 Salerno, Italy
| | - Agostino Cilibrizzi
- Institute of Pharmaceutical Science, King's College London, Stamford Street, London SE1 9NH, UK
- Centre for Therapeutic Innovation, University of Bath, Bath BA2 7AY, UK
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113
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K M K, N U, S K. Conformational dynamics and ribosomal interactions of Bacillus subtilis Obg in various nucleotide-bound states: Insights from molecular dynamics simulation. Int J Biol Macromol 2024; 279:135337. [PMID: 39241998 DOI: 10.1016/j.ijbiomac.2024.135337] [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: 05/27/2024] [Revised: 08/24/2024] [Accepted: 09/03/2024] [Indexed: 09/09/2024]
Abstract
Obg, a GTPase, binds to the premature 50S ribosomal subunit and facilitates recruitment of rproteins and rRNA processing to form the mature 50S subunit. This binding depends on nucleotide-induced conformational changes (GDP/GTP). However, the mechanism by which Obg undergoes conformational changes to associate with the premature 50S subunit is unknown. Therefore, 1000 ns molecular dynamics simulations were conducted to investigate this mechanism. Visualization of the simulated trajectory showed that in GDP and GTP-bound states, the C-domain moved towards the SwI region, while in GTP-Mg2+ and ppGpp-bound states, the C-domain shifted towards the N-tails. Further, positioning these conformations of Obg on the 50S subunit suggests possible mechanisms by which the GTP-Mg2+ bound state is responsible for recruiting rprotein, as well as the impact of the absence of Mg2+ in the GTP-bound state. Furthermore, the study provides insights into the conformational changes that may lead to the dissociation of the GDP-bound state from the 50S subunit and explores the potential role of the ppGpp-bound state in inhibiting 70S ribosome formation. Additionally, RMSF and community network analyses reveal how internal dynamics and intricate connections within Obg affect C-domain motion.
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Affiliation(s)
- Kavya K M
- Department of Studies in Physics, University of Mysore, Mysuru, India.
| | - Upendra N
- Center for Research and Innovations, Faculty of Natural Sciences, Adichunchanagiri University, B.G.Nagara, India.
| | - Krishnaveni S
- Department of Studies in Physics, University of Mysore, Mysuru, India.
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114
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Tsai HC, Xu J, Guo Z, Yi Y, Tian C, Que X, Giese T, Lee TS, York DM, Ganguly A, Pan A. Improvements in Precision of Relative Binding Free Energy Calculations Afforded by the Alchemical Enhanced Sampling (ACES) Approach. J Chem Inf Model 2024. [PMID: 39225694 DOI: 10.1021/acs.jcim.4c00464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Accurate in silico predictions of how strongly small molecules bind to proteins, such as those afforded by relative binding free energy (RBFE) calculations, can greatly increase the efficiency of the hit-to-lead and lead optimization stages of the drug discovery process. The success of such calculations, however, relies heavily on their precision. Here, we show that a recently developed alchemical enhanced sampling (ACES) approach can consistently improve the precision of RBFE calculations on a large and diverse set of proteins and small molecule ligands. The addition of ACES to conventional RBFE calculations lowered the average hysteresis by over 35% (0.3-0.4 kcal/mol) and the average replicate spread by over 25% (0.2-0.3 kcal/mol) across a set of 10 protein targets and 213 small molecules while maintaining similar or improved accuracy. We show in atomic detail how ACES improved convergence of several representative RBFE calculations through enhancing the sampling of important slowly transitioning ligand degrees of freedom.
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Affiliation(s)
- Hsu-Chun Tsai
- TandemAI, New York, New York 10036, United States
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, and Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - James Xu
- TandemAI, New York, New York 10036, United States
| | - Zhenyu Guo
- TandemAI, New York, New York 10036, United States
| | - Yinhui Yi
- TandemAI, New York, New York 10036, United States
| | - Chuan Tian
- TandemAI, New York, New York 10036, United States
| | - Xinyu Que
- TandemAI, New York, New York 10036, United States
| | - Timothy Giese
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, and Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Tai-Sung Lee
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, and Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Darrin M York
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, and Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Abir Ganguly
- TandemAI, New York, New York 10036, United States
| | - Albert Pan
- TandemAI, New York, New York 10036, United States
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115
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Shaalan MM, Osman EEA, Attia YM, Hammam OA, George RF, Naguib BH. Novel 3,6-Disubstituted Pyridazine Derivatives Targeting JNK1 Pathway: Scaffold Hopping and Hybridization-Based Design, Synthesis, Molecular Modeling, and In Vitro and In Vivo Anticancer Evaluation. ACS OMEGA 2024; 9:37310-37329. [PMID: 39246493 PMCID: PMC11375727 DOI: 10.1021/acsomega.4c05250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 08/11/2024] [Accepted: 08/13/2024] [Indexed: 09/10/2024]
Abstract
A series of novel 3,6-disubstituted pyridazine derivatives were designed, synthesized, and biologically evaluated as preclinical anticancer candidates. Compound 9e exhibited the highest growth inhibition against most of the NCI-60 cancer cell lines. The in vivo anticancer activity of 9e was subsequently investigated at two dose levels using the Ehrlich ascites carcinoma solid tumor animal model, where a reduction in the mean tumor volume allied with necrosis induction was reported without any signs of toxicity in the treated groups. Interestingly, compound 9e was capable of downregulating c-jun N-terminal kinase-1 (JNK1) gene expression and curbing the protein levels of its phosphorylated form, in parallel with a reduction in its downstream targets, namely, c-Jun and c-Fos in tumors, along with restoring p53 activity. Furthermore, molecular docking and dynamics simulations were carried out to predict the binding mode of 9e and prove its stability in the JNK1 binding pocket.
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Affiliation(s)
- Mai M Shaalan
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, The British University in Egypt, Al-Sherouk City, Cairo-Suez Desert Road, Cairo 11837, Egypt
| | - Essam Eldin A Osman
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, Cairo 11562, Egypt
| | - Yasmeen M Attia
- Pharmacology Department, Faculty of Pharmacy, The British University in Egypt, Al-Sherouk City, Cairo-Suez Desert Road, Cairo 11837, Egypt
| | - Olfat A Hammam
- Pathology Department, Theodor Bilharz Research Institute, Imbaba, Giza 12411, Egypt
| | - Riham F George
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, Cairo 11562, Egypt
| | - Bassem H Naguib
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, The British University in Egypt, Al-Sherouk City, Cairo-Suez Desert Road, Cairo 11837, Egypt
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, Cairo 11562, Egypt
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116
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Blanco-González A, Wurl A, Mendes Ferreira T, Piñeiro Á, Garcia-Fandino R. Simulating Bacterial Membrane Models at the Atomistic Level: A Force Field Comparison. J Chem Theory Comput 2024. [PMID: 39226695 DOI: 10.1021/acs.jctc.4c00204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Molecular dynamics (MD) simulations are currently an indispensable tool to understand both the dynamic and nanoscale organization of cell membrane models. A large number of quantitative parameters can be extracted from these simulations, but their reliability is determined by the quality of the employed force field and the simulation parameters. Much of the work on parametrizing and optimizing force fields for biomembrane modeling has been focused on homogeneous bilayers with a single phospholipid type. However, these may not perform effectively or could even be unsuitable for lipid mixtures commonly employed in membrane models. This work aims to fill this gap by comparing MD simulation results of several bacterial membrane models using different force fields and simulation parameters, namely, CHARMM36, Slipids, and GROMOS-CKP. Furthermore, the hydrogen isotope exchange (HIE) method, combined with GROMOS-CKP (GROMOS-H2Q), was also tested to check for the impact of this acceleration strategy on the performance of the force field. A common set of simulation parameters was employed for all of the force fields in addition to those corresponding to the original parametrization of each of them. Furthermore, new experimental order parameter values determined from NMR of several lipid mixtures are also reported to compare them with those determined from MD simulations. Our results reveal that most of the calculated physical properties of bacterial membrane models from MD simulations are substantially force field and lipid composition dependent. Some lipid mixtures exhibit nearly ideal behaviors, while the interaction of different lipid types in other mixtures is highly synergistic. None of the employed force fields seem to be clearly superior to the other three, each having its own strengths and weaknesses. Slipids are notably effective at replicating the order parameters for all acyl chains, including those in lipid mixtures, but they offer the least accurate results for headgroup parameters. Conversely, CHARMM provides almost perfect estimates for the order parameters of the headgroups but tends to overestimate those of the lipid tails. The GROMOS parametrizations deliver reasonable order parameters for entire lipid molecules, including multicomponent bilayers, although they do not reach the accuracy of Slipids for tails or CHARMM for headgroups. Importantly, GROMOS-H2Q stands out for its computational efficiency, being at least 3 times faster than GROMOS, which is already faster than both CHARMM and Slipids. In turn, GROMOS-H2Q yields much higher compressibilities compared to all other parametrizations.
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Affiliation(s)
- Alexandre Blanco-González
- Facultad de Física, University of Santiago de Compostela (USC), 15782 Santiago de Compostela, Spain
- Singular Research Centre in Chemical Biology and Molecular Materials, (CIQUS), Organic Chemistry Department, University of Santiago de Compostela (USC), 15782 Santiago de Compostela, Spain
- MD.USE Innovations S.L, Edificio Emprendia, 15782 Santiago de Compostela, Spain
| | - Anika Wurl
- Institute of Physics, Faculty of Natural Sciences II, Betty-Heimann-Str. 7, 06120 Halle/Saale, Germany
| | - Tiago Mendes Ferreira
- Institute of Physics, Faculty of Natural Sciences II, Betty-Heimann-Str. 7, 06120 Halle/Saale, Germany
| | - Ángel Piñeiro
- Facultad de Física, University of Santiago de Compostela (USC), 15782 Santiago de Compostela, Spain
| | - Rebeca Garcia-Fandino
- Singular Research Centre in Chemical Biology and Molecular Materials, (CIQUS), Organic Chemistry Department, University of Santiago de Compostela (USC), 15782 Santiago de Compostela, Spain
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117
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Wang H, Xie C, Deng B, Ding J, Li N, Kou Z, Jin M, He J, Wang Q, Wen H, Zhang J, Zhou Q, Chen S, Chen X, Yuan TF, Zhu S. Structural basis for antibody-mediated NMDA receptor clustering and endocytosis in autoimmune encephalitis. Nat Struct Mol Biol 2024:10.1038/s41594-024-01387-3. [PMID: 39227720 DOI: 10.1038/s41594-024-01387-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 08/07/2024] [Indexed: 09/05/2024]
Abstract
Antibodies against N-methyl-D-aspartate receptors (NMDARs) are most frequently detected in persons with autoimmune encephalitis (AE) and used as diagnostic biomarkers. Elucidating the structural basis of monoclonal antibody (mAb) binding to NMDARs would facilitate the development of targeted therapy for AE. Here, we reconstructed nanodiscs containing green fluorescent protein-fused NMDARs to label and sort individual immune B cells from persons with AE and further cloned and identified mAbs against NMDARs. This allowed cryo-electron microscopy analysis of NMDAR-Fab complexes, revealing that autoantibodies bind to the R1 lobe of the N-terminal domain of the GluN1 subunit. Small-angle X-ray scattering studies demonstrated NMDAR-mAb stoichiometry of 2:1 or 1:2, structurally suitable for mAb-induced clustering and endocytosis of NMDARs. Importantly, these mAbs reduced the surface NMDARs and NMDAR-mediated currents, without tonically affecting NMDAR channel gating. These structural and functional findings imply that the design of neutralizing antibody binding to the R1 lobe of NMDARs represents a potential therapy for AE treatment.
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Affiliation(s)
- Han Wang
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chun Xie
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Bo Deng
- Department of Neurology, Huashan Hospital and Institute of Neurology, National Center for Neurological Disorders, Fudan University, Shanghai, China
| | - Jingjun Ding
- Shanghai Key Laboratory of Psychotic Disorders, Brain Health Institute, National Center for Mental Disorders, Shanghai Mental Health Center, Shanghai Jiaotong University School of Medicine and School of Psychology, Shanghai, China
| | - Na Li
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China
| | - Zengwei Kou
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Mengmeng Jin
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jie He
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | | | - Han Wen
- DP Technology, Beijing, China
| | - Jinbao Zhang
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Qinming Zhou
- Department of Neurology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Sheng Chen
- Department of Neurology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.
| | - Xiangjun Chen
- Department of Neurology, Huashan Hospital and Institute of Neurology, National Center for Neurological Disorders, Fudan University, Shanghai, China.
| | - Ti-Fei Yuan
- Shanghai Key Laboratory of Psychotic Disorders, Brain Health Institute, National Center for Mental Disorders, Shanghai Mental Health Center, Shanghai Jiaotong University School of Medicine and School of Psychology, Shanghai, China.
| | - Shujia Zhu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
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118
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Oh M, Rosa M, Xie H, Khelashvili G. Automated collective variable discovery for MFSD2A transporter from molecular dynamics simulations. Biophys J 2024; 123:2934-2955. [PMID: 38932456 PMCID: PMC11393714 DOI: 10.1016/j.bpj.2024.06.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 06/03/2024] [Accepted: 06/24/2024] [Indexed: 06/28/2024] Open
Abstract
Biomolecules often exhibit complex free energy landscapes in which long-lived metastable states are separated by large energy barriers. Overcoming these barriers to robustly sample transitions between the metastable states with classical molecular dynamics (MD) simulations presents a challenge. To circumvent this issue, collective variable (CV)-based enhanced sampling MD approaches are often employed. Traditional CV selection relies on intuition and prior knowledge of the system. This approach introduces bias, which can lead to incomplete mechanistic insights. Thus, automated CV detection is desired to gain a deeper understanding of the system/process. Analysis of MD data with various machine-learning algorithms, such as principal component analysis (PCA), support vector machine, and linear discriminant analysis (LDA) based approaches have been implemented for automated CV detection. However, their performance has not been systematically evaluated on structurally and mechanistically complex biological systems. Here, we applied these methods to MD simulations of the MFSD2A (Major Facilitator Superfamily Domain 2A) lysolipid transporter in multiple functionally relevant metastable states with the goal of identifying optimal CVs that would structurally discriminate these states. Specific emphasis was on the automated detection and interpretive power of LDA-based CVs. We found that LDA methods, which included a novel gradient descent-based multiclass harmonic variant, termed GDHLDA, we developed here, outperform PCA in class separation, exhibiting remarkable consistency in extracting CVs critical for distinguishing metastable states. Furthermore, the identified CVs included features previously associated with conformational transitions in MFSD2A. Specifically, conformational shifts in transmembrane helix 7 and in residue Y294 on this helix emerged as critical features discriminating the metastable states in MFSD2A. This highlights the effectiveness of LDA-based approaches in automatically extracting from MD trajectories CVs of functional relevance that can be used to drive biased MD simulations to efficiently sample conformational transitions in the molecular system.
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Affiliation(s)
- Myongin Oh
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York
| | - Margarida Rosa
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York
| | - Hengyi Xie
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York
| | - George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York; Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York.
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119
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Liao J, Wu M, Gao J, Chen C. Calculation of solvation force in molecular dynamics simulation by deep-learning method. Biophys J 2024; 123:2830-2838. [PMID: 38444159 PMCID: PMC11393703 DOI: 10.1016/j.bpj.2024.02.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/31/2024] [Accepted: 02/29/2024] [Indexed: 03/07/2024] Open
Abstract
Electrostatic calculations are generally used in studying the thermodynamics and kinetics of biomolecules in solvent. Generally, this is performed by solving the Poisson-Boltzmann equation on a large grid system, a process known to be time consuming. In this study, we developed a deep neural network to predict the decomposed solvation free energies and forces of all atoms in a molecule. To train the network, the internal coordinates of the molecule were used as the input data, and the solvation free energies along with transformed atomic forces from the Poisson-Boltzmann equation were used as labels. Both the training and prediction tasks were accelerated on GPU. Formal tests demonstrated that our method can provide reasonable predictions for small molecules when the network is well-trained with its simulation data. This method is suitable for processing lots of snapshots of molecules in a long trajectory. Moreover, we applied this method in the molecular dynamics simulation with enhanced sampling. The calculated free energy landscape closely resembled that obtained from explicit solvent simulations.
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Affiliation(s)
- Jun Liao
- Biomolecular Physics and Modeling Group, School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Mincong Wu
- Biomolecular Physics and Modeling Group, School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Junyong Gao
- Biomolecular Physics and Modeling Group, School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Changjun Chen
- Biomolecular Physics and Modeling Group, School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China.
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120
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Franke L, Globisch C, Karakurt MC, Stephan T, Peter C. Atomistic Simulations Reveal Crucial Role of Metal Ions for Ligand Binding in Guanidine-I Riboswitch. Macromol Rapid Commun 2024:e2400606. [PMID: 39225633 DOI: 10.1002/marc.202400606] [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: 07/25/2024] [Revised: 08/22/2024] [Indexed: 09/04/2024]
Abstract
Riboswitches are structured ribonucleic acid (RNA) segments that act as specific sensors for small molecules in bacterial metabolism. Due to the flexible nature of these highly charged macromolecules, molecular dynamics simulations are instrumental to investigating the mechanistic details of their regulatory function. In the present study, the guanidine-I riboswitch serves as an example of how atomistic simulations can shed light on the effect of ions on the structure and dynamics of RNA and on ligand binding. Relying on two orthologous crystal structures from different bacterial species, it is demonstrated how the ion setup crucially determines whether the simulation yields meaningful insights into the conformational stability of the RNA, functionally relevant residues and RNA-ligand interactions. The ion setup in this context includes diffuse ions in solution and bound ions associated directly with the RNA, in particular a triad of 2 Mg2+ ions and a K+ ion in close proximity to the guanidinium binding site. A detailed investigation of the binding pocket reveals that the K+ from the ion triad plays a decisive role in stabilizing the ligand binding by stabilizing important localized interactions, which in turn contribute to the overall shape of the folded state of the RNA.
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Affiliation(s)
- Leon Franke
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Christoph Globisch
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Mehmet Can Karakurt
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Theresa Stephan
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Christine Peter
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
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Chiu PL, Orjuela JD, de Groot BL, Aponte Santamaría C, Walz T. Structure and dynamics of cholesterol-mediated aquaporin-0 arrays and implications for lipid rafts. eLife 2024; 12:RP90851. [PMID: 39222068 PMCID: PMC11368405 DOI: 10.7554/elife.90851] [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] [Indexed: 09/04/2024] Open
Abstract
Aquaporin-0 (AQP0) tetramers form square arrays in lens membranes through a yet unknown mechanism, but lens membranes are enriched in sphingomyelin and cholesterol. Here, we determined electron crystallographic structures of AQP0 in sphingomyelin/cholesterol membranes and performed molecular dynamics (MD) simulations to establish that the observed cholesterol positions represent those seen around an isolated AQP0 tetramer and that the AQP0 tetramer largely defines the location and orientation of most of its associated cholesterol molecules. At a high concentration, cholesterol increases the hydrophobic thickness of the annular lipid shell around AQP0 tetramers, which may thus cluster to mitigate the resulting hydrophobic mismatch. Moreover, neighboring AQP0 tetramers sandwich a cholesterol deep in the center of the membrane. MD simulations show that the association of two AQP0 tetramers is necessary to maintain the deep cholesterol in its position and that the deep cholesterol increases the force required to laterally detach two AQP0 tetramers, not only due to protein-protein contacts but also due to increased lipid-protein complementarity. Since each tetramer interacts with four such 'glue' cholesterols, avidity effects may stabilize larger arrays. The principles proposed to drive AQP0 array formation could also underlie protein clustering in lipid rafts.
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Affiliation(s)
- Po-Lin Chiu
- Department of Cell Biology, Harvard Medical SchoolBostonUnited States
| | - Juan D Orjuela
- Max Planck Tandem Group in Computational Biophysics, Universidad de los AndesBogotáColombia
- Biomedical Engineering Department, Universidad de los AndesBogotáColombia
| | - Bert L de Groot
- Computational Biomolecular Dynamics Group, Max Planck Institute for Multidisciplinary SciencesGöttingenGermany
| | - Camilo Aponte Santamaría
- Max Planck Tandem Group in Computational Biophysics, Universidad de los AndesBogotáColombia
- Molecular Biomechanics Group, Heidelberg Institute for Theoretical StudiesHeidelbergGermany
| | - Thomas Walz
- Department of Cell Biology, Harvard Medical SchoolBostonUnited States
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Raguraman V, Chauhan L, Gehlot P, Kongkham B, Hariprasad P. Computational insights into the role of structurally diverse plant secondary metabolites as inhibitors against Imidazole Glycerol Phosphate Dehydratase of Mycobacterium tuberculosis. J Biomol Struct Dyn 2024; 42:8159-8171. [PMID: 37578041 DOI: 10.1080/07391102.2023.2245486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 07/28/2023] [Indexed: 08/15/2023]
Abstract
Mycobacterium tuberculosis (Mtb) is one of the major causes of death worldwide and there is a pressing need for the development of novel drug leads. The Imidazole Glycerol Phosphate Dehydratase (IGPD) of Mtb is one of the key enzymes in the histidine biosynthesis pathway and has been recognized as the potentially underexploited drug target for anti-tuberculosis treatment. In the present study, 6063 structurally diverse plant secondary metabolites (PSM) were screened for their efficiency in inhibiting the catalytic activity of IGPD through molecular docking. The top 150 PSMs with the lowest binding energy represent the chemical classes, including Tannins (34%), Flavonoid Glycosides (14%), Terpene Glycosides (10%), Steroid Lactones (9.3%), Flavonoids (6.6%), Steroidal Glycosides (4.6%), etc. Bismahanine, Ashwagandhanolide, and Daurisoline form stable IGPD-inhibitor complexes with binding free energies of -291.3 ± 16.5, -279.0 ± 25.0, and -279.8 ± 17.6 KJ/mol, respectively, as determined by molecular dynamics simulations. These PSM demonstrated strong H-bond interactions with the amino acid residues Ile279, Arg281, and Lys276 in the catalytic region of IGPD, as revealed by structural snapshots. On the basis of our findings, these three PSM could be considered as possible leads against IGPD and should be explored in vitro and in vivo.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Vasantharaja Raguraman
- Environmental Biotechnology Laboratory, Centre for Rural Development and Technology, Indian Institute of Technology Delhi, New Delhi, India
| | - Leena Chauhan
- Environmental Biotechnology Laboratory, Centre for Rural Development and Technology, Indian Institute of Technology Delhi, New Delhi, India
| | - Priyanka Gehlot
- Environmental Biotechnology Laboratory, Centre for Rural Development and Technology, Indian Institute of Technology Delhi, New Delhi, India
| | - Bhani Kongkham
- Environmental Biotechnology Laboratory, Centre for Rural Development and Technology, Indian Institute of Technology Delhi, New Delhi, India
| | - P Hariprasad
- Environmental Biotechnology Laboratory, Centre for Rural Development and Technology, Indian Institute of Technology Delhi, New Delhi, India
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Deshpande A, Bryer AJ, Andino-Moncada JR, Shi J, Hong J, Torres C, Harel S, Francis AC, Perilla JR, Aiken C, Rousso I. Elasticity of the HIV-1 core facilitates nuclear entry and infection. PLoS Pathog 2024; 20:e1012537. [PMID: 39259747 PMCID: PMC11419384 DOI: 10.1371/journal.ppat.1012537] [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: 05/28/2024] [Revised: 09/23/2024] [Accepted: 08/27/2024] [Indexed: 09/13/2024] Open
Abstract
HIV-1 infection requires passage of the viral core through the nuclear pore of the cell, a process that depends on functions of the viral capsid. Recent studies have shown that HIV-1 cores enter the nucleus prior to capsid disassembly. Interactions of the viral capsid with the nuclear pore complex are necessary but not sufficient for nuclear entry, and the mechanism by which the viral core traverses the comparably sized nuclear pore is unknown. Here we show that the HIV-1 core is highly elastic and that this property is linked to nuclear entry and infectivity. Using atomic force microscopy-based approaches, we found that purified wild type cores rapidly returned to their normal conical morphology following a severe compression. Results from independently performed molecular dynamic simulations of the mature HIV-1 capsid also revealed its elastic property. Analysis of four HIV-1 capsid mutants that exhibit impaired nuclear entry revealed that the mutant viral cores are brittle. Adaptation of two of the mutant viruses in cell culture resulted in additional substitutions that restored elasticity and rescued infectivity and nuclear entry. We also show that capsid-targeting compound PF74 and the antiviral drug Lenacapavir reduce core elasticity and block HIV-1 nuclear entry at concentrations that preserve interactions between the viral core and the nuclear envelope. Our results indicate that elasticity is a fundamental property of the HIV-1 core that enables nuclear entry, thereby facilitating infection. These results provide new insights into the role of the capsid in HIV-1 nuclear entry and the antiviral mechanisms of HIV-1 capsid inhibitors.
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Affiliation(s)
- Akshay Deshpande
- Ben-Gurion University of the Negev, Department of Physiology and Cell Biology, Beer Sheva, Israel
| | - Alexander J. Bryer
- University of Delaware, Department of Chemistry and Biochemistry, Newark, Delaware, United States of America
| | - Jonathan R. Andino-Moncada
- Florida State University, Institute of Molecular Biophysics, Tallahassee, Florida, United States of America
| | - Jiong Shi
- Vanderbilt University Medical Center, Department of Pathology, Microbiology and Immunology, Nashville, Tennessee, United States of America
| | - Jun Hong
- Vanderbilt University Medical Center, Department of Pathology, Microbiology and Immunology, Nashville, Tennessee, United States of America
| | - Cameron Torres
- Vanderbilt University Medical Center, Department of Pathology, Microbiology and Immunology, Nashville, Tennessee, United States of America
| | - Shimon Harel
- Ben-Gurion University of the Negev, Department of Physiology and Cell Biology, Beer Sheva, Israel
| | - Ashwanth C. Francis
- Florida State University, Institute of Molecular Biophysics, Tallahassee, Florida, United States of America
- Florida State University, Department of Biological Sciences, Tallahassee, Florida, United States of America
| | - Juan R. Perilla
- University of Delaware, Department of Chemistry and Biochemistry, Newark, Delaware, United States of America
| | - Christopher Aiken
- Vanderbilt University Medical Center, Department of Pathology, Microbiology and Immunology, Nashville, Tennessee, United States of America
| | - Itay Rousso
- Ben-Gurion University of the Negev, Department of Physiology and Cell Biology, Beer Sheva, Israel
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Gianvincenzo PD, Leyes MF, Boonkam K, Puentes AF, Reyes SG, Nardi AN, Olivieri A, Pummarin S, Kamonsutthipaijit N, Amenitsch H, Ritacco H, D'Abramo M, Ortore MG, Boonla C, Moya SE. Supramolecular citrate poly allylamine hydrochloride nanoparticles for citrate delivery and calcium oxalate nanocrystal dissolution. J Colloid Interface Sci 2024; 669:667-678. [PMID: 38733878 DOI: 10.1016/j.jcis.2024.04.185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/24/2024] [Accepted: 04/25/2024] [Indexed: 05/13/2024]
Abstract
HYPOTHESIS Renal calculi (kidney stones) are mainly made by calcium oxalate and can cause different complications including malfunction of the kidney. The most important urinary stone inhibitors are citrate molecules. Unfortunately, the amount of citrate reaching the kidney after oral ingestion is low. We hypothesized that nanoparticles of polyallylamine hydrochloride (CIT-PAH) carrying citrate ions could simultaneously deliver citrates while PAH would complex oxalate triggering dissolution and removal of CaOx nanocrystals. EXPERIMENTS We successfully prepared nanoparticles of citrate ions with polyallylamine hydrochloride (CIT-PAH), PAH with oxalate (OX-PAH) and characterize them by Small Angle X ray Scattering (SAXS), Transmission Electron Microscopy (TEM), Dynamic Light Scattering (DLS) and NMR. Dissolution of CaOx nanocrystals in presence of CIT-PAH have been followed with Wide Angle Xray Scattering (WAXS), DLS and Confocal Raman Microscopy. Raman spectroscopy was used to study the dissolution of crystals in synthetic urine samples. The release of citrate from CIT-PAH was followed by diffusion NMR. Molecular dynamics (MD) simulations were carried out to study the interaction of CIT and OX ions with PAH. FINDINGS CIT-PAH nanoparticles dissolves CaOx nanocrystals as shown by NMR, DLS, TEM and WAXS in water and by Raman spectroscopy in artificial human urine. WAXS and Raman show that the crystal structure of CaOx disappears in the presence of CIT-PAH. DLS shows that the time required for CaOX dissolution will depend on the concentration of CIT-PAH NPs. NMR proves that citrate ions are released from the CIT PAH NPs during CaOX dissolution, MD simulations showed that oxalates exhibit a stronger interaction for PAH than citrate, explaining the removal of oxalate ions and replacement of the citrate in the polymer nanoparticles.
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Affiliation(s)
- Paolo Di Gianvincenzo
- Soft Matter Nanotechnology Group, CIC biomaGUNE, Basque Research and Technological Alliance (BART), Paseo Miramón 182 C, 20014 San Sebastian, Spain
| | - Marcos Fernandez Leyes
- Soft Matter Nanotechnology Group, CIC biomaGUNE, Basque Research and Technological Alliance (BART), Paseo Miramón 182 C, 20014 San Sebastian, Spain; Instituto de Física del Sur (IFISUR), Departamento de Física, Universidad Nacional del Sur (UNS), CONICET, Av. L. N. Alem 1253, B8000CPB Bahía Blanca, Argentina
| | - Kamonchat Boonkam
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, 10330 Bangkok, Thailand
| | - Alejandro Fábrega Puentes
- Soft Matter Nanotechnology Group, CIC biomaGUNE, Basque Research and Technological Alliance (BART), Paseo Miramón 182 C, 20014 San Sebastian, Spain
| | - Santiago Gimenez Reyes
- Soft Matter Nanotechnology Group, CIC biomaGUNE, Basque Research and Technological Alliance (BART), Paseo Miramón 182 C, 20014 San Sebastian, Spain; Instituto de Física del Sur (IFISUR), Departamento de Física, Universidad Nacional del Sur (UNS), CONICET, Av. L. N. Alem 1253, B8000CPB Bahía Blanca, Argentina
| | | | - Alessio Olivieri
- Chemistry Department, "La Sapienza" University of Rome, P. le A. Moro 5, 00185 Rome, Italy
| | - Siwanut Pummarin
- Soft Matter Nanotechnology Group, CIC biomaGUNE, Basque Research and Technological Alliance (BART), Paseo Miramón 182 C, 20014 San Sebastian, Spain; Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, 10330 Bangkok, Thailand
| | | | - Heinz Amenitsch
- Institute of Inorganic Chemistry, Graz University of Technology, Stremayergasse 9/V, Graz, Austria
| | - Hernan Ritacco
- Instituto de Física del Sur (IFISUR), Departamento de Física, Universidad Nacional del Sur (UNS), CONICET, Av. L. N. Alem 1253, B8000CPB Bahía Blanca, Argentina
| | - Marco D'Abramo
- Chemistry Department, "La Sapienza" University of Rome, P. le A. Moro 5, 00185 Rome, Italy
| | - Maria Grazia Ortore
- Department of Life and Environmental Science, Marche Polytechnic University, Ancona I-60131, Italy
| | - Chanchai Boonla
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, 10330 Bangkok, Thailand
| | - Sergio E Moya
- Soft Matter Nanotechnology Group, CIC biomaGUNE, Basque Research and Technological Alliance (BART), Paseo Miramón 182 C, 20014 San Sebastian, Spain.
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125
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Chaudhuri D, Majumder S, Datta J, Giri K. Exploring the chemical space for potential inhibitors against cell surface binding protein of Mpox virus using molecular fingerprint based screening approach. J Biomol Struct Dyn 2024; 42:7160-7173. [PMID: 37480263 DOI: 10.1080/07391102.2023.2238087] [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: 12/27/2022] [Accepted: 07/13/2023] [Indexed: 07/23/2023]
Abstract
Mpox virus is the latest member of the Poxviridae family of which small pox virus is a member. Monekypox virus has led to thousands of infections across the globe. Poxvirus gains entry into the cell making use of glycosaminoglycans like chondroitin sulphate and heparan sulphate. The interaction of the Mpox virus protein E8L also called cell surface binding protein is crucial for host cell attachment, membrane fusion and viral entry into the host cell leading to establishment of infection thus making this protein a very attractive therapeutic target. In this study we have tried to utilize the chondroitin sulphate binding groove present in the protein and identify molecules which are structurally similar to chondroitin sulphate. These molecules can thus occupy the same pocket but with a better binding affinity than chondroitin sulphate in order to outcompete the latter molecule from binding to the E8L protein and thus prevent it from performing its function. This study may pave the way for development of highly efficient therapeutics against the Mpox virus and further curb its infective potential.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | - Joyeeta Datta
- Department of Life Sciences, Presidency University, Kolkata, India
| | - Kalyan Giri
- Department of Life Sciences, Presidency University, Kolkata, India
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126
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Kim T, Lee Y, Lim H, Kim Y, Cho H, Namkung W, Han G. Discovery of Protease-activated receptor 2 antagonists derived from phenylalanine for the treatment of breast cancer. Bioorg Chem 2024; 150:107496. [PMID: 38850590 DOI: 10.1016/j.bioorg.2024.107496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/22/2024] [Accepted: 05/23/2024] [Indexed: 06/10/2024]
Abstract
Protease-activated receptor 2 (PAR2) has garnered attention as a potential therapeutic target in breast cancer. PAR2 is implicated in the activation of extracellular signal-regulated kinase 1/2 (ERK 1/2) via G protein and beta-arrestin pathways, contributing to the proliferation and metastasis of breast cancer cells. Despite the recognized role of PAR2 in breast cancer progression, clinically effective PAR2 antagonists remain elusive. To address this unmet clinical need, we synthesized and evaluated a series of novel compounds that target the orthosteric site of PAR2. Using in silico docking simulations, we identified compound 9a, an optimized derivative of compound 1a ((S)-N-(1-(benzylamino)-1-oxo-3-phenylpropan-2-yl)benzamide), which exhibited enhanced PAR2 antagonistic activity. Subsequent molecular dynamics simulations comparing 9a with the partial agonist 9d revealed that variations in ligand-induced conformational changes and interactions dictated whether the compound acted as an antagonist or agonist of PAR2. The results of this study suggest that further development of 9a could contribute to the advancement of PAR2 antagonists as potential therapeutic agents for breast cancer.
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Affiliation(s)
- Taegun Kim
- Department of Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Yechan Lee
- Department of Pharmacy, College of Pharmacy, Yonsei University, Incheon 21983, Republic of Korea
| | - Hocheol Lim
- Department of Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Yeonhwa Kim
- Graduate Program of Industrial Pharmaceutical Science, College of Pharmacy, Yonsei University, Incheon 21983, Republic of Korea
| | - Haeun Cho
- Graduate Program of Industrial Pharmaceutical Science, College of Pharmacy, Yonsei University, Incheon 21983, Republic of Korea
| | - Wan Namkung
- Department of Pharmacy, College of Pharmacy, Yonsei University, Incheon 21983, Republic of Korea
| | - Gyoonhee Han
- Department of Biotechnology, Yonsei University, Seoul 03722, Republic of Korea; Department of Pharmacy, College of Pharmacy, Yonsei University, Incheon 21983, Republic of Korea.
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127
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Yang R, Bernardino K, Xiao X, Gomes WR, Mattoso DA, Kotov NA, Bogdan P, de Moura AF. Graph Theoretical Description of Phase Transitions in Complex Multiscale Phases with Supramolecular Assemblies. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2402464. [PMID: 38952077 DOI: 10.1002/advs.202402464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 05/15/2024] [Indexed: 07/03/2024]
Abstract
Phase transitions are typically quantified using order parameters, such as crystal lattice distances and radial distribution functions, which can identify subtle changes in crystalline materials or high-contrast phases with large structural differences. However, the identification of phases with high complexity, multiscale organization and of complex patterns during the structural fluctuations preceding phase transitions, which are essential for understanding the system pathways between phases, is challenging for those traditional analyses. Here, it is shown that for two model systems- thermotropic liquid crystals and a lyotropic water/surfactant mixtures-graph theoretical (GT) descriptors can successfully identify complex phases combining molecular and nanoscale levels of organization that are hard to characterize with traditional methodologies. Furthermore, the GT descriptors also reveal the pathways between the different phases. Specifically, centrality parameters and node-based fractal dimension quantify the system behavior preceding the transitions, capturing fluctuation-induced breakup of aggregates and their long-range cooperative interactions. GT parameterization can be generalized for a wide range of chemical systems and be instrumental for the growth mechanisms of complex nanostructures.
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Affiliation(s)
- Ruochen Yang
- Ming Hsieh Department of Electrical and Computer Engineering, University of Southern California, Los Angeles, CA, 90089, USA
- Center of Complex Particle Systems (COMPASS), Ann Arbor, MI, 48109-2102, USA
| | - Kalil Bernardino
- Department of Chemistry, Federal University of São Carlos, São Carlos, SP, 13565-905, Brazil
| | - Xiongye Xiao
- Ming Hsieh Department of Electrical and Computer Engineering, University of Southern California, Los Angeles, CA, 90089, USA
- Center of Complex Particle Systems (COMPASS), Ann Arbor, MI, 48109-2102, USA
| | - Weverson R Gomes
- Department of Chemistry, Federal University of São Carlos, São Carlos, SP, 13565-905, Brazil
| | - Davi A Mattoso
- Department of Chemistry, Federal University of São Carlos, São Carlos, SP, 13565-905, Brazil
| | - Nicholas A Kotov
- Center of Complex Particle Systems (COMPASS), Ann Arbor, MI, 48109-2102, USA
- Department of Chemical Engineering, Department of Materials Science and Engineering, Biointerfaces Institute, University of Michigan, Ann Arbor, MI, 48109-2102, USA
| | - Paul Bogdan
- Ming Hsieh Department of Electrical and Computer Engineering, University of Southern California, Los Angeles, CA, 90089, USA
- Center of Complex Particle Systems (COMPASS), Ann Arbor, MI, 48109-2102, USA
| | - André F de Moura
- Department of Chemistry, Federal University of São Carlos, São Carlos, SP, 13565-905, Brazil
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128
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Yuce M, Ates B, Yasar NI, Sungur FA, Kurkcuoglu O. A computational workflow to determine drug candidates alternative to aminoglycosides targeting the decoding center of E. coli ribosome. J Mol Graph Model 2024; 131:108817. [PMID: 38976944 DOI: 10.1016/j.jmgm.2024.108817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/08/2024] [Accepted: 07/03/2024] [Indexed: 07/10/2024]
Abstract
The global antibiotic resistance problem necessitates fast and effective approaches to finding novel inhibitors to treat bacterial infections. In this study, we propose a computational workflow to identify plausible high-affinity compounds from FDA-approved, investigational, and experimental libraries for the decoding center on the small subunit 30S of the E. coli ribosome. The workflow basically consists of two molecular docking calculations on the intact 30S, followed by molecular dynamics (MD) simulations coupled with MM-GBSA calculations on a truncated ribosome structure. The parameters used in the molecular docking suits, Glide and AutoDock Vina, as well as in the MD simulations with Desmond were carefully adjusted to obtain expected interactions for the ligand-rRNA complexes. A filtering procedure was followed, considering a fingerprint based on aminoglycoside's binding site on the 30S to obtain seven hit compounds either with different clinical usages or aminoglycoside derivatives under investigation, suggested for in vitro studies. The detailed workflow developed in this study promises an effective and fast approach for the estimation of binding free energies of large protein-RNA and ligand complexes.
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Affiliation(s)
- Merve Yuce
- Istanbul Technical University, Department of Chemical Engineering, Istanbul, 34469, Turkey.
| | - Beril Ates
- Istanbul Technical University, Department of Chemical Engineering, Istanbul, 34469, Turkey.
| | - Nesrin Isil Yasar
- Istanbul Technical University, Computational Science and Engineering Division, Informatics Institute, Istanbul, 34469, Turkey.
| | - Fethiye Aylin Sungur
- Istanbul Technical University, Computational Science and Engineering Division, Informatics Institute, Istanbul, 34469, Turkey.
| | - Ozge Kurkcuoglu
- Istanbul Technical University, Department of Chemical Engineering, Istanbul, 34469, Turkey.
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129
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Nabi F, Ahmad O, Khan A, Hassan MN, Hisamuddin M, Malik S, Chaari A, Khan RH. Natural compound plumbagin based inhibition of hIAPP revealed by Markov state models based on MD data along with experimental validations. Proteins 2024; 92:1070-1084. [PMID: 38497314 DOI: 10.1002/prot.26682] [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: 12/07/2023] [Revised: 02/26/2024] [Accepted: 02/28/2024] [Indexed: 03/19/2024]
Abstract
Human islet amyloid polypeptide (amylin or hIAPP) is a 37 residue hormone co-secreted with insulin from β cells of the pancreas. In patients suffering from type-2 diabetes, amylin self-assembles into amyloid fibrils, ultimately leading to the death of the pancreatic cells. However, a research gap exists in preventing and treating such amyloidosis. Plumbagin, a natural compound, has previously been demonstrated to have inhibitory potential against insulin amyloidosis. Our investigation unveils collapsible regions within hIAPP that, upon collapse, facilitates hydrophobic and pi-pi interactions, ultimately leading to aggregation. Intriguingly plumbagin exhibits the ability to bind these specific collapsible regions, thereby impeding the aforementioned interactions that would otherwise drive hIAPP aggregation. We have used atomistic molecular dynamics approach to determine secondary structural changes. MSM shows metastable states forming native like hIAPP structure in presence of PGN. Our in silico results concur with in vitro results. The ThT assay revealed a striking 50% decrease in fluorescence intensity at a 1:1 ratio of hIAPP to Plumbagin. This finding suggests a significant inhibition of amyloid fibril formation by plumbagin, as ThT fluorescence directly correlates with the presence of these fibrils. Further TEM images revealed disappearance of hIAPP fibrils in plumbagin pre-treated hIAPP samples. Also, we have shown that plumbagin disrupts the intermolecular hydrogen bonding in hIAPP fibrils leading to an increase in the average beta strand spacing, thereby causing disaggregation of pre-formed fibrils demonstrating overall disruption of the aggregation machinery of hIAPP. Our work is the first to report a detailed atomistic simulation of 22 μs for hIAPP. Overall, our studies put plumbagin as a potential candidate for both preventive and therapeutic candidate for hIAPP amyloidosis.
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Affiliation(s)
- Faisal Nabi
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Owais Ahmad
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Adeeba Khan
- Zakir Hussain College of Engineering and Technology, Aligarh Muslim University, Aligarh, India
| | - Md Nadir Hassan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Malik Hisamuddin
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Sadia Malik
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Ali Chaari
- Premedical Division, Weill Cornell Medicine Qatar, Qatar Foundation, Doha, Qatar
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
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130
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Ansari S, Zia MK, Ahsan H, Hashmi MA, Khan FH. Binding characteristics and conformational changes in alpha-2-macroglobulin by the dietary flavanone naringenin: biophysical and computational approach. J Biomol Struct Dyn 2024; 42:7485-7500. [PMID: 37498152 DOI: 10.1080/07391102.2023.2240420] [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: 05/18/2023] [Accepted: 07/18/2023] [Indexed: 07/28/2023]
Abstract
In the present study, we investigated the interaction of alpha-2-macroglobulin (α2M) with naringenin using multi-spectroscopic, molecular docking, and molecular simulation approaches to identify the functional changes and structural variations in the α2M structure. Our study suggests that naringenin compromised α2M anti-proteinase activity. The results of absorption spectroscopy and fluorescence measurement showed that naringenin-α2M formed a complex with a binding constant of (kb)∼104, indicative of moderate binding. The value of ΔG° in the binding indicates the process to be spontaneous and the major force responsible to be hydrophobic interaction. The findings of FRET reveal the binding distance between naringenin and the amino acids of α2M was 2.82 nm. The secondary structural analysis of α2M with naringenin using multi-spectroscopic methods like synchronous fluorescence, red-edge excitation shift (REES), FTIR, and CD spectra further confirmed the significant conformational alterations in the protein. Molecular docking approach reveals the interactions between naringenin and α2M to be hydrogen bonds, van der Waals forces, and pi interactions, which considerably favour and stabilise the binding. Molecular dynamics modelling simulations also supported the steady binding with the least RMSD deviations. Our study suggests that naringenin interacts with α2M to alter its confirmation and compromise its activity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sana Ansari
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
| | - Mohammad Khalid Zia
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
| | - Haseeb Ahsan
- Department of Biochemistry, Faculty of Dentistry, Jamia Millia Islamia, New Delhi, India
| | - Md Amiruddin Hashmi
- Interdisciplinary Biotechnology Unit, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, UP, India
| | - Fahim H Khan
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
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Hassan HA, Muhammed SS, Al-Khdhairawi A, Abdelwahab SF, Abdel-Rahman IM, Abdelhamid MM. Unraveling effective extracellular signal-regulated kinase 2 inhibitors: a de novo drug design strategy enhanced by in-depth in silico analyses. J Biomol Struct Dyn 2024; 42:7906-7916. [PMID: 37584104 DOI: 10.1080/07391102.2023.2246563] [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: 05/02/2023] [Accepted: 07/23/2023] [Indexed: 08/17/2023]
Abstract
Extracellular signal-regulated kinase 2 (ERK-2) is a serine/threonine protein kinase in eukaryotic cells and belongs to the mitogen-activated protein kinase (MAPK) family. An activated form of ERK-2 phosphorylates substrates in the nucleus or cytoplasm and causes specific proteins to be expressed or activated, regulating cell proliferation, differentiation and other functions. Caffeic acid (3,4 - dihydroxy cinnamic acid), as previously reported, directly interacts with ERK-2 and reduces its effects in vitro. It is also reported to have a variety of pharmacological effects, including anti-inflammatory, immunomodulatory, antioxidant and anticancer activities. In the current study, a deep-learning protocol was employed to develop effective 100 compounds by modifying the chemical structure of DHC to improve its inhibitory performance against ERK-2. Calculations of physicochemical properties for those compounds revealed that 20 compounds had drug scores better than DHC (≥ 80%). Following that, molecular docking calculations were performed on the selected compounds and DHC. The obtained data revealed that five compounds had docking scores better than DHC (≥ -5.9 kcal/mol). Moreover, data from molecular mechanics and the Poisson - Boltzmann surface area (MM/PBSA) binding energy over 200 ns MD simulation confirmed that Cmd-1 and Cmd-4 exhibited higher stability with ΔGbinding of -40.8 and -49.1 kcal/mol, respectively, which is better than DHC (-35.1 kcal/mol). Finally, various energetic and structural studies showed the high stability of the two generated compounds within the active site of ERK-2. This study highlights the potential use of Cmd-1 and Cmd-4 as promising anti-ERK-2 drug candidates.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Heba Ali Hassan
- Department of Pharmacognosy, Faculty of Pharmacy, Sohag University, Sohag, Egypt
| | - Sara S Muhammed
- Faculty of Pharmacy for girls, AlAzhar University, Banha, Egypt
| | - Ahmad Al-Khdhairawi
- Department of Biological Science and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Sayed F Abdelwahab
- Department of Pharmaceutics and Industrial Pharmacy, College of Pharmacy, Taif University, Taif, Saudi Arabia
| | - Islam M Abdel-Rahman
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Deraya University, New-Minia, Egypt
| | - Mahmoud M Abdelhamid
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Al-Azhar University, Assiut, Egypt
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Islam MR, Biswas S, Amena U, Rahman M, Islam S, Islam MA, Saleh MA, Hassan HM, Al‐Emam A, Zaki MEA. Modified oxymatrine as novel therapeutic inhibitors against Monkeypox and Marburg virus through computational drug design approaches. J Cell Mol Med 2024; 28:e70116. [PMID: 39340487 PMCID: PMC11437895 DOI: 10.1111/jcmm.70116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 08/06/2024] [Accepted: 09/17/2024] [Indexed: 09/30/2024] Open
Abstract
Global impact of viral diseases specially Monkeypox (mpox) and Marburg virus, emphasizing the urgent need for effective drug interventions. Oxymatrine is an alkaloid which has been selected and modified using various functional groups to enhance its efficacy. The modifications were evaluated using various computatioanal analysis such as pass prediction, molecular docking, ADMET, and molecular dynamic simulation. Mpox and Marburg virus were chosen as target diseases based on their maximum pass prediction spectrum against viral disease. After that, molecular docking, dynamic simulation, DFT, calculation and ADMET prediction were determined. The main objective of this study was to enhance the efficacy of oxymatrine derivatives through functional group modifications and computational analyses to develop effective drug candidates against mpox and Marburg viruses. The calculated binding affinities indicated strong interactions against both mpox virus and Marburg virus. After that, the molecular dynamic simulation was conducted at 100 ns, which confirmed the stability of the binding interactions between the modified oxymatrine derivatives and target proteins. Then, the modified oxymatrine derivatives conducted theoretical ADMET profiling, which demonstrated their potential for effective drug development. Moreover, HOMO-LUMO calculation was performed to understand the chemical reactivity and physicochemical properties of compounds. This computational analysis indicated that modified oxymatrine derivatives for the treatment of mpox and Marburg virus suggested effective drug candidates based on their binding affinity, drug-like properties, stability and chemical reactivity. However, further experimental validation is necessary to confirm their clinical value and efficacy as therapeutic candidates.
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Affiliation(s)
- Md. Rezaul Islam
- Department of Pharmacy, Faculty of Allied Health SciencesDaffodil International UniversityAshuliaDhakaBangladesh
| | - Suvro Biswas
- Department of Genetic Engineering and BiotechnologyUniversity of RajshahiRajshahiBangladesh
| | - Ummy Amena
- Department of Pharmacy, Faculty of Life & Earth SciencesJagannath UniversityDhakaBangladesh
| | - Miadur Rahman
- Department of Pharmaceutical SciencesNorth South UniversityDhakaBangladesh
| | - Shirmin Islam
- Department of Genetic Engineering and BiotechnologyUniversity of RajshahiRajshahiBangladesh
| | - Md. Ariful Islam
- Department of Genetic Engineering and BiotechnologyUniversity of RajshahiRajshahiBangladesh
| | - Md. Abu Saleh
- Department of Genetic Engineering and BiotechnologyUniversity of RajshahiRajshahiBangladesh
| | - Hesham M. Hassan
- Department of Pathology, College of MedicineKing Khalid UniversityAsirSaudi Arabia
| | - Ahmed Al‐Emam
- Department of Pathology, College of MedicineKing Khalid UniversityAsirSaudi Arabia
| | - Magdi E. A. Zaki
- Department of Chemistry, College of ScienceImam Mohammad Ibn Saud Islamic University RiyadhRiyadhSaudi Arabia
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133
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Osmaniye D, Yuva O, Sağlık BN, Levent S, Ozkay Y, Kaplancıklı ZA. Design, synthesis, evaluation of biological activities and molecular docking and dynamic studies of novel acetazolamide analog compounds. J Biomol Struct Dyn 2024; 42:7243-7256. [PMID: 37490028 DOI: 10.1080/07391102.2023.2239930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 07/16/2023] [Indexed: 07/26/2023]
Abstract
Modification of drugs used in the clinic is a frequently used method with regards to medicinal chemistry in the development of new drugs. Acetazolamide is a drug in clinical use as a CA inhibitor. Within the scope of this study, the 'N-(5-sulfamoyl-1,3,4-thiadiazol-2-yl) acetamide' structure, which is acetazolamide residue, was kept constant; various mercaptan substitutions were made from methylene adjacent to the carbonyl group in the structure. Compounds 4c, 4d, 4e, 4 g, 4h, 4i, and 4j exhibited inhibitor activity against CA enzyme with IC50=0.238 ± 0.010, 0.161 ± 0.007, 0.067 ± 0.002, 0.084 ± 0.003, 0.033 ± 0.001, 0.049 ± 0.002 and 0.187 ± 0.008 µM, respectively. The intermolecular interactions of the promising compounds with aromatase enzyme were investigated through the SP docking approach, which revealed significant binding interaction energies associated with these compounds. To measure the stability of the compounds in the enzyme active site, dynamic studies were performed at 100 ns. In addition to the RMSD, RMSF parameters, the interaction ratios of compound 4h with amino acids in the enzyme active site and the interaction histograms were also investigated. The results obtained are quite promising. Continuous interactions were exhibited with Thr199, Glu106, His96, His94 and His119, which are important for the CA enzyme.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Derya Osmaniye
- Department of Pharmaceutical Chemistry, Anadolu University, Eskişehir, Turkey
- Central Research Laboratory (MERLAB), Anadolu University, Eskişehir, Turkey
| | - Onur Yuva
- Department of Pharmaceutical Technology, Anadolu University, Eskişehir, Turkey
| | - Begüm Nurpelin Sağlık
- Department of Pharmaceutical Chemistry, Anadolu University, Eskişehir, Turkey
- Central Research Laboratory (MERLAB), Anadolu University, Eskişehir, Turkey
| | - Serkan Levent
- Department of Pharmaceutical Chemistry, Anadolu University, Eskişehir, Turkey
- Central Research Laboratory (MERLAB), Anadolu University, Eskişehir, Turkey
| | - Yusuf Ozkay
- Department of Pharmaceutical Chemistry, Anadolu University, Eskişehir, Turkey
- Central Research Laboratory (MERLAB), Anadolu University, Eskişehir, Turkey
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134
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Yang B, Zhao T, Ji S, Liu Y, Xu M, Lu B. Molecular dynamics simulations of the interfacial behaviors and photo-oxidation of phytosterol under different emulsion oil content. Food Chem 2024; 451:139292. [PMID: 38663239 DOI: 10.1016/j.foodchem.2024.139292] [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: 12/01/2023] [Revised: 04/05/2024] [Accepted: 04/07/2024] [Indexed: 05/26/2024]
Abstract
Phytosterol, recognized for its health benefits, is predominantly extracted from plants and exhibits significantly reduced stability under varying light conditions. Their photooxidation is significantly influenced by emulsion interfaces. This study examined the mechanism of interface structure on phytosterol photooxidation with unparalleled molecular precision, utilizing molecular dynamics simulations and experimental procedures. Hydrogen bonding between the hydroxyl group at the C3 position of phytosterols and water molecules, coupled with van der Waals forces between the hydrophobic regions and the oil phase, induced phytosterol molecules to disperse toward the interface. The elevated polarity of the oil phase, specifically in tributyrin, facilitated the permeation of water molecules into the oil phase. This was achieved by diminishing the emulsion's interfacial tension, thereby fostering the development of more interface or micelles, and accelerating the photooxidation process of phytosterols. These simulations unraveled that the preponderance of phytosterol distribution is localized and oxidized at the oil-water interface.
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Affiliation(s)
- Bowen Yang
- National Engineering Laboratory of Intelligent Food Technology and Equipment, Key Laboratory for Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, Key Laboratory for Agro-Products Nutritional Evaluation of Ministry of Agriculture and Rural Affairs, Zhejiang Key Laboratory for Agro-Food Processing, Ningbo Research Institute, Fuli Institute of Food Science, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Tian Zhao
- National Engineering Laboratory of Intelligent Food Technology and Equipment, Key Laboratory for Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, Key Laboratory for Agro-Products Nutritional Evaluation of Ministry of Agriculture and Rural Affairs, Zhejiang Key Laboratory for Agro-Food Processing, Ningbo Research Institute, Fuli Institute of Food Science, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Shengyang Ji
- National Engineering Laboratory of Intelligent Food Technology and Equipment, Key Laboratory for Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, Key Laboratory for Agro-Products Nutritional Evaluation of Ministry of Agriculture and Rural Affairs, Zhejiang Key Laboratory for Agro-Food Processing, Ningbo Research Institute, Fuli Institute of Food Science, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Yan Liu
- National Engineering Laboratory of Intelligent Food Technology and Equipment, Key Laboratory for Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, Key Laboratory for Agro-Products Nutritional Evaluation of Ministry of Agriculture and Rural Affairs, Zhejiang Key Laboratory for Agro-Food Processing, Ningbo Research Institute, Fuli Institute of Food Science, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Minghao Xu
- National Engineering Laboratory of Intelligent Food Technology and Equipment, Key Laboratory for Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, Key Laboratory for Agro-Products Nutritional Evaluation of Ministry of Agriculture and Rural Affairs, Zhejiang Key Laboratory for Agro-Food Processing, Ningbo Research Institute, Fuli Institute of Food Science, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Baiyi Lu
- National Engineering Laboratory of Intelligent Food Technology and Equipment, Key Laboratory for Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, Key Laboratory for Agro-Products Nutritional Evaluation of Ministry of Agriculture and Rural Affairs, Zhejiang Key Laboratory for Agro-Food Processing, Ningbo Research Institute, Fuli Institute of Food Science, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China.
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135
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Li Y, Liu Y, Yang B, Li G, Chu H. Polarizable atomic multipole-based force field for cholesterol. J Biomol Struct Dyn 2024; 42:7747-7757. [PMID: 37565356 DOI: 10.1080/07391102.2023.2245045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 07/21/2023] [Indexed: 08/12/2023]
Abstract
Cholesterol is one of the essential component of lipid in membrane. We present a polarizable atomic multipole force field (FF) for the molecular dynamic simulation of cholesterol. The FF building process follows the computational framework as the atomic multipole optimized energetics for biomolecular applications (AMOEBA) model. In this framework, the electronics parameters, including atomic monopole moments, dipole moments, and quadrupole moments calculated from ab initio calculations in the gas phase, are applied to represent the charge distribution. Furthermore, the many-body polarization is modeled by following the same pattern of distributed atomic polarizabilities. Then, the bilayers composed of two typical phospholipid molecules, 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), in a range of different cholesterol concentrations are built and implemented by molecular dynamics (MD) simulations based on the proposed polarizable FF. The simulation results are statistically analyzed to validate the feasibility of the proposed FF. The structural properties of the bilayers are calculated to compare with the related experimental values. The MD values show the same trend of experimental values changes.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yan Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, China
| | - Ye Liu
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, China
| | - Boya Yang
- Dalian Municipal Central Hospital, Liaoning, China
| | - Guohui Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, China
| | - Huiying Chu
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, China
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136
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Steuer J, Sinn M, Eble F, Rütschlin S, Böttcher T, Hartig JS, Peter C. Cooperative binding of bivalent ligands yields new insights into the guanidine-II riboswitch. NAR Genom Bioinform 2024; 6:lqae132. [PMID: 39323654 PMCID: PMC11423145 DOI: 10.1093/nargab/lqae132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 08/23/2024] [Accepted: 09/12/2024] [Indexed: 09/27/2024] Open
Abstract
Riboswitches are involved in regulating the gene expression in bacteria. They are located within the untranslated regions of bacterial messenger RNA and function as switches by adjusting their shape, depending on the presence or absence of specific ligands. To decipher the fundamental aspects of bacterial gene control, it is therefore important to understand the mechanisms that underlie these conformational switches. To this end, a combination of an experimental binding study, molecular simulations and machine learning has been employed to obtain insights into the conformational changes and structural dynamics of the guanidine-II riboswitch. By exploiting the design of a bivalent ligand, we were able to study ligand binding in the aptamer dimer at the molecular level. Spontaneous ligand-binding events, which are usually difficult to simulate, were observed and the contributing factors are described. These findings were further confirmed by in vivo experiments, where the cooperative binding effects of the bivalent ligands resulted in increased binding affinity compared to the native guanidinium ligand. Beyond ligand binding itself, the simulations revealed a novel, ligand-dependent base-stacking interaction outside of the binding pocket that stabilizes the riboswitch.
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Affiliation(s)
- Jakob Steuer
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany
- Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, 78457 Konstanz, Germany
| | - Malte Sinn
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany
| | - Franziska Eble
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany
| | - Sina Rütschlin
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany
- Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, 78457 Konstanz, Germany
| | - Thomas Böttcher
- Faculty of Chemistry, Institute for Biological Chemistry & Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystems Science, University of Vienna, Josef-Holaubek-Platz 2 (UZA II), 1090 Vienna, Austria
| | - Jörg S Hartig
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany
- Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, 78457 Konstanz, Germany
| | - Christine Peter
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany
- Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, 78457 Konstanz, Germany
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137
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Blum MM, Schmeißer W, Dentzel M, Thiermann H, John H. The blistering warfare agent O-mustard (agent T) generates protein-adducts with human serum albumin useful for biomedical verification of exposure and forms intramolecular cross-links. Anal Bioanal Chem 2024:10.1007/s00216-024-05501-8. [PMID: 39215775 DOI: 10.1007/s00216-024-05501-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 08/14/2024] [Accepted: 08/16/2024] [Indexed: 09/04/2024]
Abstract
The highly blistering sulfur mustard analogue agent T (bis(2-chloroethylthioethyl) ether), also known as O-mustard or oxy-mustard, is a common impurity in military grade sulfur mustard (SM) and a component of mixtures such as "HT" that are still found in old munitions. Together with sesquimustard (Q), it is the most important SM analogue and tightly regulated as a Schedule 1 chemical under the Chemical Weapons Convention. We report the adducts of T with nucleophilic Cys34 and other residues in human serum albumin (HSA) formed in vitro. A micro liquid chromatography electrospray ionization high-resolution tandem-mass spectrometry method (µLC-ESI MS/HR MS) was developed for the detection and identification of biomarker peptides alkylated by a T-derived hydroxyethylthioethyloxyethylthioethyl (HETEOETE)-moiety (as indicated by an asterisk below). Following proteolysis of T-exposed human plasma with pronase, the dipeptide Cys34*Pro and the single amino acid residue His* were produced. The use of proteinase K yielded Cys34*ProPhe and the use of pepsin generated ValThrGlu48*Phe, AlaGlu230*ValSerLysLeu, and LeuGlyMet329*Phe. Corresponding peptide-adducts of SM and Q were detected in a common workflow that in principle allowed the estimation of the mustard or mustard composition encountered during exposure. Novel adducts of Q at the Glu230 and Met239 residues were detected and are reported accordingly. Based on molecular dynamics simulations, we identified regular interactions of the Cys34(-HETEOETE)-moiety with several glutamic acid residues in HSA including Glu86, which is not an obvious interaction partner by visual inspection of the HSA crystal structure. The existence of this and other intramolecular cross-links was experimentally proven for the first time.
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Affiliation(s)
- Marc-Michael Blum
- Blum - Scientific Services, Björnsonweg 70d, 22587, Hamburg, Germany
| | - Wolfgang Schmeißer
- Bundeswehr Institute of Pharmacology and Toxicology, Neuherbergstraße 11, 80937, Munich, Germany
| | - Marina Dentzel
- Bundeswehr Institute of Pharmacology and Toxicology, Neuherbergstraße 11, 80937, Munich, Germany
| | - Horst Thiermann
- Bundeswehr Institute of Pharmacology and Toxicology, Neuherbergstraße 11, 80937, Munich, Germany
| | - Harald John
- Bundeswehr Institute of Pharmacology and Toxicology, Neuherbergstraße 11, 80937, Munich, Germany.
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138
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Petruk G, Petrlova J, Samsudin F, Bond PJ, Schmidtchen A. Thrombin-derived C-terminal peptides bind and form aggregates with sulfated glycosaminoglycans. Heliyon 2024; 10:e35703. [PMID: 39229523 PMCID: PMC11369470 DOI: 10.1016/j.heliyon.2024.e35703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 07/30/2024] [Accepted: 08/01/2024] [Indexed: 09/05/2024] Open
Abstract
Glycosaminoglycans (GAGs) such as heparin and heparan sulfate (HS) play crucial roles in inflammation and wound healing, serving as regulators of growth factors and pro-inflammatory mediators. In this study, we investigated the influence of heparin/HS on thrombin proteolysis and its interaction with the generated 11 kDa thrombin-derived C-terminal peptides (TCPs). Employing various biochemical and biophysical methods, we demonstrated that 11 kDa TCPs aggregate in the presence of GAGs, including heparin, heparan sulfate, and chondroitin sulfate-B. Circular dichroism analysis demonstrated that 11 kDa TCPs, in the presence of GAGs, adopt a β-sheet structure, a finding supported by thioflavin T1 (ThT) fluorescence measurements and visualization of 11 kDa TCP-heparin complexes using transmission electron microscopy (TEM). Furthermore, our investigations revealed a stronger binding affinity between 11 kDa TCPs and GAGs with higher sulfate group contents. Congruently, in silico simulations showed that interactions between 11 kDa TCPs and heparin/HS are predominantly electrostatic in nature. Collectively, our study suggests that 11 kDa TCPs have the capacity to aggregate in the presence of GAGs, shedding light on their potential roles in inflammation and wound healing.
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Affiliation(s)
- Ganna Petruk
- Division of Dermatology and Venereology, Department of Clinical Sciences, Lund University, 22241, Lund, Sweden
| | - Jitka Petrlova
- Division of Dermatology and Venereology, Department of Clinical Sciences, Lund University, 22241, Lund, Sweden
- Department of Biomedical Science, Faculty of Health and Society, Malmö University, SE-205 06, Malmö, Sweden
| | - Firdaus Samsudin
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Peter J. Bond
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Republic of Singapore
| | - Artur Schmidtchen
- Division of Dermatology and Venereology, Department of Clinical Sciences, Lund University, 22241, Lund, Sweden
- Dermatology, Skane University Hospital, 22185, Lund, Sweden
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139
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Jani V, Sonavane U, Joshi R. Insight into structural dynamics involved in activation mechanism of full length KRAS wild type and P-loop mutants. Heliyon 2024; 10:e36161. [PMID: 39247361 PMCID: PMC11379609 DOI: 10.1016/j.heliyon.2024.e36161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 08/06/2024] [Accepted: 08/11/2024] [Indexed: 09/10/2024] Open
Abstract
KRAS protein is known to be frequently mutated in various cancers. The most common mutations being at position 12, 13 and 61. The positions 12 and 13 form part of the phosphate binding region (P-loop) of KRAS. Owing to mutation, the protein remains in continuous active state and affects the normal cellular process. Understanding the structural changes owing to mutations in GDP-bound (inactive state) and GTP-bound (active state) may help in the design of better therapeutics. To understand the structural flexibility due to the mutations specifically located at P-loop regions (G12D, G12V and G13D), extensive molecular dynamics simulations (24 μs) have been carried for both inactive (GDP-bound) and active (GTP-bound) structures for the wild type and these mutants. The study revealed that the local structural changes at the site of mutations allosterically guide changes in distant regions of the protein through hydrogen bond and hydrophobic signalling network. The dynamic cross correlation analysis and the comparison of the correlated motions among different systems manifested that changes in SW-I, SW-II, α3 and the loop preceding α3 affects the interactions of GDP/GTP with different regions of the protein thereby affecting its hydrolysis. Further, the Markov state modelling analysis confirmed that the mutations, especially G13D imparts rigidity to structure compared to wild type and thus limiting its conformational state in either intermediate state or active state. The study suggests that along with SW-I and SW-II regions, the loop region preceding the α3 helix and α3 helix are also involved in affecting the hydrolysis of nucleotides and may be considered while designing therapeutics against KRAS.
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Affiliation(s)
- Vinod Jani
- Centre for Development of Advanced Computing (C-DAC), Panchavati, Pashan, Pune, India
| | - Uddhavesh Sonavane
- Centre for Development of Advanced Computing (C-DAC), Panchavati, Pashan, Pune, India
| | - Rajendra Joshi
- Centre for Development of Advanced Computing (C-DAC), Panchavati, Pashan, Pune, India
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140
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Liang Y, Zhang Y, Huang Y, Xu C, Chen J, Zhang X, Huang B, Gan Z, Dong X, Huang S, Li C, Jia S, Zhang P, Yuan Y, Zhang H, Wang Y, Yuan B, Bao Y, Xiao S, Xiong M. Helicity-directed recognition of bacterial phospholipid via radially amphiphilic antimicrobial peptides. SCIENCE ADVANCES 2024; 10:eadn9435. [PMID: 39213359 PMCID: PMC11364095 DOI: 10.1126/sciadv.adn9435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 07/25/2024] [Indexed: 09/04/2024]
Abstract
The fundamental differences in phospholipids between bacterial and mammalian cell membranes present remarkable opportunities for antimicrobial design. However, it is challenging to distinguish bacterial anionic phospholipid phosphatidylglycerol (PG) from mammalian anionic phosphatidylserine (PS) with the same net charge. Here, we report a class of radially amphiphilic α helix antimicrobial peptides (RAPs) that can selectively discriminate PG from PS, relying on the helix structure. The representative RAP, L10-MMBen, can direct the rearrangement of PG vesicles into a lamellar structure with its helix axis parallel to the PG membrane surface. The helical structure imparts both the thermodynamic and kinetic advantages of L10-MMBen/PG assembly, and the hiding of hydrophobic regions in RAPs is crucial for PG recognition. L10-MMBen exhibits high selectivity against bacteria depending on PG recognition, showing low in vivo toxicity and significant treatment efficacy in mice infection models. Our study introduces a helicity-direct bacterial phospholipid recognition paradigm for designing highly selective antimicrobial peptides.
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Affiliation(s)
- Yangbin Liang
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou 511442, P. R. China
- National Engineering Research Centre for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou 510006, P. R. China
| | - Yuhao Zhang
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou 511442, P. R. China
- National Engineering Research Centre for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou 510006, P. R. China
| | - Yu Huang
- CAS Key Laboratory of Soft Matter Chemistry, Department of Polymer Science and Engineering, Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Cheng Xu
- Songshan Lake Materials Laboratory, Institute of Physics, Chinese Academy of Sciences, Dongguan, 523808, P. R. China
| | - Jingxian Chen
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou 511442, P. R. China
- National Engineering Research Centre for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou 510006, P. R. China
| | - Xinshuang Zhang
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou 511442, P. R. China
- National Engineering Research Centre for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou 510006, P. R. China
| | - Bingchuan Huang
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou 511442, P. R. China
- National Engineering Research Centre for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou 510006, P. R. China
| | - Zhanhui Gan
- South China Advanced Institute for Soft Matter Science and Technology, School of Emergent Soft Matter, South China University of Technology, Guangzhou 510640, China
| | - Xuehui Dong
- South China Advanced Institute for Soft Matter Science and Technology, School of Emergent Soft Matter, South China University of Technology, Guangzhou 510640, China
| | - Songyin Huang
- Biotherapy Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, P. R. China
| | - Chengrun Li
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou 511442, P. R. China
- National Engineering Research Centre for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou 510006, P. R. China
| | - Shuyi Jia
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou 511442, P. R. China
- National Engineering Research Centre for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou 510006, P. R. China
| | - Pengfei Zhang
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou 511442, P. R. China
| | - Yueling Yuan
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou 511442, P. R. China
- Key Laboratory of Biomedical Materials and Engineering of the Ministry of Education, South China University of Technology, Guangzhou, Guangdong 510006, P. R. China
| | - Houbing Zhang
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou 511442, P. R. China
| | - Yucai Wang
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, P. R. China
| | - Bing Yuan
- Songshan Lake Materials Laboratory, Institute of Physics, Chinese Academy of Sciences, Dongguan, 523808, P. R. China
| | - Yan Bao
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, P. R. China
| | - Shiyan Xiao
- CAS Key Laboratory of Soft Matter Chemistry, Department of Polymer Science and Engineering, Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Menghua Xiong
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou 511442, P. R. China
- National Engineering Research Centre for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou 510006, P. R. China
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Kaur A, Kumar A, Kumari G, Muduli R, Das M, Kundu R, Mukherjee S, Majumdar T. Rational design and computational evaluation of a multi-epitope vaccine for monkeypox virus: Insights into binding stability and immunological memory. Heliyon 2024; 10:e36154. [PMID: 39247273 PMCID: PMC11380015 DOI: 10.1016/j.heliyon.2024.e36154] [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: 08/05/2024] [Accepted: 08/11/2024] [Indexed: 09/10/2024] Open
Abstract
Multi-epitope vaccines strategically tackle rapidly mutating viruses by targeting diverse epitopes from different proteins, providing a comprehensive and adaptable immune protection approach for enhanced coverage against various viral variants. This research employs a comprehensive approach that includes the mapping of immune cells activating epitopes derived from the six structural glycoproteins (A29L, A30L, A35R, L1R, M1R, and E8L) of Monkeypox virus (Mpox). A total of 7 T-cells-specific epitopes, 13 B-cells-specific epitopes, and 5 IFN-γ activating epitopes were forecasted within these glycoproteins. The selection process focused on epitopes indicating high immunogenicity and favorable binding affinity with multiple MHC alleles. Following this, a vaccine has been formulated by incorporating the chosen epitopes, alongside adjuvants (PADRE peptide) and various linkers (EAAAK, GPGPG, and AAY). The physicochemical properties and 3D structure of the multi-epitope hybrid vaccine were analysed for characterization. MD simulations were employed to predict the binding stability between the vaccine and various pathogen recognition receptors such as TLRs (TLR1, TLR2, TLR4, and TLR6), as well as both class I and II MHC, achieved through hydrogen bonding and hydrophobic interactions. Through in silico cloning and immune simulation, it was observed that the multi-epitopes vaccine induced a robust memory immune response upon booster doses, forecasting protective immunity upon viral challenge. This protective immunity was characterized by the production of IgM + IgG antibodies, along with release of inflammatory cytokines like IFN-γ, and IL12, and the activation of various immune cells. This study offers valuable insights into the potential of a multi-epitope vaccine targeting the Mpox virus.
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Affiliation(s)
| | - Amit Kumar
- National Institute of Immunology, New Delhi, India
| | | | | | - Mayami Das
- National Institute of Immunology, New Delhi, India
| | - Rakesh Kundu
- Department of Zoology, Visva-Bharati University, Santiniketan, West Bengal, India
| | - Suprabhat Mukherjee
- Department of Animal Science, Kazi Nazrul University, Asansol, West Bengal, India
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142
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Nelson AD, Wang L, Laffey KG, Becher LRE, Parks CA, Hoffmann MM, Galeano BK, Mangalam A, Teixeiro E, White TA, Schrum AG, Cannon JF, Gil D. Rigid crosslinking of the CD3 complex leads to superior T cell stimulation. Front Immunol 2024; 15:1434463. [PMID: 39281668 PMCID: PMC11392757 DOI: 10.3389/fimmu.2024.1434463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Accepted: 08/07/2024] [Indexed: 09/18/2024] Open
Abstract
Functionally bivalent non-covalent Fab dimers (Bi-Fabs) specific for the TCR/CD3 complex promote CD3 signaling on T cells. While comparing functional responses to stimulation with Bi-Fab, F(ab')2 or mAb specific for the same CD3 epitope, we observed fratricide requiring anti-CD3 bridging of adjacent T cells. Surprisingly, anti-CD3 Bi-Fab ranked first in fratricide potency, followed by anti-CD3 F(ab')2 and anti-CD3 mAb. Low resolution structural studies revealed anti-CD3 Bi-Fabs and F(ab')2 adopt similar global shapes with CD3-binding sites oriented outward. However, under molecular dynamic simulations, anti-CD3 Bi-Fabs crosslinked CD3 more rigidly than F(ab')2. Furthermore, molecular modelling of Bi-Fab and F(ab')2 binding to CD3 predicted crosslinking of T cell antigen receptors located in opposing plasma membrane domains, a feature fitting with T cell fratricide observed. Thus, increasing rigidity of Fab-CD3 crosslinking between opposing effector-target pairs may result in stronger T cell effector function. These findings could guide improving clinical performance of bi-specific anti-CD3 drugs.
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Affiliation(s)
- Alfreda D Nelson
- Department of Surgery, School of Medicine, University of Missouri, Columbia, MO, United States
| | - Liangyu Wang
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, United States
| | - Kimberly G Laffey
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, United States
| | - Laura R E Becher
- Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN, United States
| | - Christopher A Parks
- Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN, United States
| | - Michele M Hoffmann
- Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN, United States
| | - Belinda K Galeano
- Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN, United States
| | - Ashutosh Mangalam
- Department of Pathology, University of Iowa, Iowa City, IA, United States
| | - Emma Teixeiro
- Department of Surgery, School of Medicine, University of Missouri, Columbia, MO, United States
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, United States
| | - Tommi A White
- Department of Biochemistry, University of Missouri, Columbia, MO, United States
| | - Adam G Schrum
- Department of Surgery, School of Medicine, University of Missouri, Columbia, MO, United States
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, United States
- Department of Biomedical, Biological and Medical Engineering, College of Engineering, University of Missouri, Columbia, MO, United States
| | - John F Cannon
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, United States
| | - Diana Gil
- Department of Surgery, School of Medicine, University of Missouri, Columbia, MO, United States
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, United States
- Department of Biomedical, Biological and Medical Engineering, College of Engineering, University of Missouri, Columbia, MO, United States
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143
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Gwyther REA, Côté S, Lee CS, Miao H, Ramakrishnan K, Palma M, Dafydd Jones D. Optimising CNT-FET biosensor design through modelling of biomolecular electrostatic gating and its application to β-lactamase detection. Nat Commun 2024; 15:7482. [PMID: 39209826 PMCID: PMC11362306 DOI: 10.1038/s41467-024-51325-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 08/02/2024] [Indexed: 09/04/2024] Open
Abstract
Carbon nanotube field effect transistors (CNT-FET) hold great promise as next generation miniaturised biosensors. One bottleneck is modelling how proteins, with their distinctive electrostatic surfaces, interact with the CNT-FET to modulate conductance. Using advanced sampling molecular dynamics combined with non-canonical amino acid chemistry, we model protein electrostatic potential imparted on single walled CNTs (SWCNTs). We focus on using β-lactamase binding protein (BLIP2) as the receptor as it binds the antibiotic degrading enzymes, β-lactamases (BLs). BLIP2 is attached via the single selected residue to SWCNTs using genetically encoded phenyl azide photochemistry. Our devices detect two different BLs, TEM-1 and KPC-2, with each BL generating distinct conductance profiles due to their differing surface electrostatic profiles. Changes in conductance match the model electrostatic profile sampled by the SWCNTs on BL binding. Thus, our modelling approach combined with residue-specific receptor attachment could provide a general approach for systematic CNT-FET biosensor construction.
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Affiliation(s)
- Rebecca E A Gwyther
- Molecular Biosciences Division, School of Biosciences Cardiff University, Cardiff, UK
| | - Sébastien Côté
- Département de Physique, Faculté des Arts et des Sciences, Université de Montréal, Montréal, QC, Canada.
- Département de Physique, Cégep de Saint-Jérôme, Saint-Jérôme, QC, Canada.
| | - Chang-Seuk Lee
- Department of Chemistry, Queen Mary University of London, London, UK
- Department of Chemistry, Seoul Women's University, Seoul, Republic of Korea
| | - Haosen Miao
- Department of Chemistry, Queen Mary University of London, London, UK
| | - Krithika Ramakrishnan
- Molecular Biosciences Division, School of Biosciences Cardiff University, Cardiff, UK
| | - Matteo Palma
- Department of Chemistry, Queen Mary University of London, London, UK.
| | - D Dafydd Jones
- Molecular Biosciences Division, School of Biosciences Cardiff University, Cardiff, UK.
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144
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Singh G, Bhopale A, Khatri S, Prakash P, Kumar R, Singh S, Singh S. Structural characterization of DNA-binding domain of essential mammalian protein TTF 1. Biosci Rep 2024; 44:BSR20240800. [PMID: 39115563 PMCID: PMC11358750 DOI: 10.1042/bsr20240800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 07/31/2024] [Accepted: 08/02/2024] [Indexed: 08/29/2024] Open
Abstract
Transcription Termination Factor 1 (TTF1) is a multifunctional mammalian protein with vital roles in various cellular processes, including Pol I-mediated transcription initiation and termination, pre-rRNA processing, chromatin remodelling, DNA damage repair, and polar replication fork arrest. It comprises two distinct functional regions; the N-terminal regulatory region (1-445 aa), and the C-terminal catalytic region (445-859 aa). The Myb domain located at the C-terminal region is a conserved DNA binding domain spanning from 550 to 732 aa (183 residues). Despite its critical role in various cellular processes, the physical structure of TTF1 remains unsolved. Attempts to purify the functional TTF1 protein have been unsuccessful till date. Therefore, we focused on characterizing the Myb domain of this essential protein. We started with predicting a 3-D model of the Myb domain using homology modelling, and ab-initio method. We then determined its stability through MD simulation in an explicit solvent. The model predicted is highly stable, which stabilizes at 200ns. To experimentally validate the computational model, we cloned and expressed the codon optimized Myb domain into a bacterial expression vector and purified the protein to homogeneity. Further, characterization of the protein shows that, Myb domain is predominantly helical (65%) and is alone sufficient to bind the Sal Box DNA. This is the first-ever study to report a complete in silico model of the Myb domain, which is physically characterized. The above study will pave the way towards solving the atomic structure of this essential mammalian protein.
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Affiliation(s)
- Gajender Singh
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, UP 221005, India
| | - Abhinetra Jagdish Bhopale
- Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (B.H.U.), Varanasi, UP 221005, India
| | - Saloni Khatri
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, UP 221005, India
| | - Prashant Prakash
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, UP 221005, India
| | - Rajnish Kumar
- Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (B.H.U.), Varanasi, UP 221005, India
| | - Sukh Mahendra Singh
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, UP 221005, India
| | - Samarendra Kumar Singh
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, UP 221005, India
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145
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Adriaenssens E, Schaar S, Cook ASI, Stuke JFM, Sawa-Makarska J, Nguyen TN, Ren X, Schuschnig M, Romanov J, Khuu G, Lazarou M, Hummer G, Hurley JH, Martens S. Reconstitution of BNIP3/NIX-mediated autophagy reveals two pathways and hierarchical flexibility of the initiation machinery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.28.609967. [PMID: 39253418 PMCID: PMC11383309 DOI: 10.1101/2024.08.28.609967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
Selective autophagy is a lysosomal degradation pathway that is critical for maintaining cellular homeostasis by disposing of harmful cellular material. While the mechanisms by which soluble cargo receptors recruit the autophagy machinery are becoming increasingly clear, the principles governing how organelle-localized transmembrane cargo receptors initiate selective autophagy remain poorly understood. Here, we demonstrate that transmembrane cargo receptors can initiate autophagosome biogenesis not only by recruiting the upstream FIP200/ULK1 complex but also via a WIPI-ATG13 complex. This latter pathway is employed by the BNIP3/NIX receptors to trigger mitophagy. Additionally, other transmembrane mitophagy receptors, including FUNDC1 and BCL2L13, exclusively use the FIP200/ULK1 complex, while FKBP8 and the ER-phagy receptor TEX264 are capable of utilizing both pathways to initiate autophagy. Our study defines the molecular rules for initiation by transmembrane cargo receptors, revealing remarkable flexibility in the assembly and activation of the autophagy machinery, with significant implications for therapeutic interventions.
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146
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Vautrin L, Lambert A, Mahdhaoui F, El Abed R, Boubaker T, Ingrosso F. Structural and Electronic Properties of Novel Azothiophene Dyes: A Multilevel Study Incorporating Explicit Solvation Effects. Molecules 2024; 29:4053. [PMID: 39274901 PMCID: PMC11397383 DOI: 10.3390/molecules29174053] [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: 07/30/2024] [Revised: 08/20/2024] [Accepted: 08/23/2024] [Indexed: 09/16/2024] Open
Abstract
Among azobenzene derivatives, azothiophenes represent a relatively recent family of compounds that exhibit similar characteristics as dyes and photoreactive systems. Their technological applications are extensive thanks to the additional design flexibility conferred by the heteroaromatic ring. In this study, we present a comprehensive investigation of the structural and electronic properties of novel dyes derived from 3-thiophenamine, utilizing a multilevel approach. We thoroughly examined the potential energy surfaces of the E and Z isomers for three molecules, each bearing different substituents on the phenyl ring at the para position relative to the diazo group. This exploration was conducted through quantum chemistry calculations at various levels of theory, employing a continuum solvent model. Subsequently, we incorporated an explicit solvent (a dimethyl sulfoxide-water mixture) to simulate the most stable isomers using classical molecular dynamics, delivering a clear picture of the local solvation structure and intermolecular interactions. Finally, a hybrid quantum mechanics/molecular mechanics (QM/MM) approach was employed to accurately describe the evolution of the solutes' properties within their environment, accounting for finite temperature effects.
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Affiliation(s)
- Laura Vautrin
- Université de Lorraine and CNRS, Laboratoire de Physique et Chimie Théoriques UMR 7019, F-54000 Nancy, France
| | - Alexandrine Lambert
- Université de Lorraine and CNRS, Laboratoire de Physique et Chimie Théoriques UMR 7019, F-54000 Nancy, France
| | - Faouzi Mahdhaoui
- Université de Lorraine and CNRS, Laboratoire de Physique et Chimie Théoriques UMR 7019, F-54000 Nancy, France
| | - Riad El Abed
- Laboratoire de Chimie Hétérocyclique, Produits Naturels et Réactivité (LR11SE39), Faculté des Sciences de Monastir, Université de Monastir, Avenue de l'Environnement, Monastir 5019, Tunisia
| | - Taoufik Boubaker
- Laboratoire de Chimie Hétérocyclique, Produits Naturels et Réactivité (LR11SE39), Faculté des Sciences de Monastir, Université de Monastir, Avenue de l'Environnement, Monastir 5019, Tunisia
| | - Francesca Ingrosso
- Université de Lorraine and CNRS, Laboratoire de Physique et Chimie Théoriques UMR 7019, F-54000 Nancy, France
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147
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Kantarcioglu I, Gaszek IK, Guclu TF, Yildiz MS, Atilgan AR, Toprak E, Atilgan C. Structural shifts in TolC facilitate Efflux-Mediated β-lactam resistance. Commun Biol 2024; 7:1051. [PMID: 39187619 PMCID: PMC11347637 DOI: 10.1038/s42003-024-06750-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 08/16/2024] [Indexed: 08/28/2024] Open
Abstract
Efflux-mediated β-lactam resistance is a major public health concern, reducing the effectiveness of β-lactam antibiotics against many bacteria. Structural analyses show the efflux protein TolC in Gram-negative bacteria acts as a channel for antibiotics, impacting bacterial susceptibility and virulence. This study examines β-lactam drug efflux mediated by TolC using experimental and computational methods. Molecular dynamics simulations of drug-free TolC reveal essential movements and key residues involved in TolC opening. A whole-gene-saturation mutagenesis assay, mutating each TolC residue and measuring fitness effects under β-lactam selection, is performed. Here we show the TolC-mediated efflux of three antibiotics: oxacillin, piperacillin, and carbenicillin. Steered molecular dynamics simulations identify general and drug-specific efflux mechanisms, revealing key positions at TolC's periplasmic entry affecting efflux motions. Our findings provide insights into TolC's structural dynamics, aiding the design of new antibiotics to overcome bacterial efflux mechanisms.
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Affiliation(s)
- Isik Kantarcioglu
- Faculty of Engineering and Natural Sciences, Sabancı University, Tuzla, Istanbul, Turkey
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ilona K Gaszek
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Tandac F Guclu
- Faculty of Engineering and Natural Sciences, Sabancı University, Tuzla, Istanbul, Turkey
| | - M Sadik Yildiz
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ali Rana Atilgan
- Faculty of Engineering and Natural Sciences, Sabancı University, Tuzla, Istanbul, Turkey
| | - Erdal Toprak
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Canan Atilgan
- Faculty of Engineering and Natural Sciences, Sabancı University, Tuzla, Istanbul, Turkey.
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148
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Mandal N, Surpeta B, Brezovsky J. Reinforcing Tunnel Network Exploration in Proteins Using Gaussian Accelerated Molecular Dynamics. J Chem Inf Model 2024; 64:6623-6635. [PMID: 39143923 DOI: 10.1021/acs.jcim.4c00966] [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: 08/16/2024]
Abstract
Tunnels are structural conduits in biomolecules responsible for transporting chemical compounds and solvent molecules from the active site. They have been shown to be present in a wide variety of enzymes across all functional and structural classes. However, the study of such pathways is experimentally challenging, because they are typically transient. Computational methods, such as molecular dynamics (MD) simulations, have been successfully proposed to explore tunnels. Conventional MD (cMD) provides structural details to characterize tunnels but suffers from sampling limitations to capture rare tunnel openings on longer time scales. Therefore, in this study, we explored the potential of Gaussian accelerated MD (GaMD) simulations to improve the exploration of complex tunnel networks in enzymes. We used the haloalkane dehalogenase LinB and its two variants with engineered transport pathways, which are not only well-known for their application potential but have also been extensively studied experimentally and computationally regarding their tunnel networks and their importance in multistep catalytic reactions. Our study demonstrates that GaMD efficiently improves tunnel sampling and allows the identification of all known tunnels for LinB and its two mutants. Furthermore, the improved sampling provided insight into a previously unknown transient side tunnel (ST). The extensive conformational landscape explored by GaMD simulations allowed us to investigate in detail the mechanism of ST opening. We determined variant-specific dynamic properties of ST opening, which were previously inaccessible due to limited sampling of cMD. Our comprehensive analysis supports multiple indicators of the functional relevance of the ST, emphasizing its potential significance beyond structural considerations. In conclusion, our research proves that the GaMD method can overcome the sampling limitations of cMD for the effective study of tunnels in enzymes, providing further means for identifying rare tunnels in enzymes with the potential for drug development, precision medicine, and rational protein engineering.
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Affiliation(s)
- Nishita Mandal
- Laboratory of Biomolecular Interactions and Transport, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, Poznan 61-614, Poland
- International Institute of Molecular and Cell Biology in Warsaw, Ks Trojdena 4, Warsaw 02-109, Poland
| | - Bartlomiej Surpeta
- Laboratory of Biomolecular Interactions and Transport, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, Poznan 61-614, Poland
- International Institute of Molecular and Cell Biology in Warsaw, Ks Trojdena 4, Warsaw 02-109, Poland
| | - Jan Brezovsky
- Laboratory of Biomolecular Interactions and Transport, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, Poznan 61-614, Poland
- International Institute of Molecular and Cell Biology in Warsaw, Ks Trojdena 4, Warsaw 02-109, Poland
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149
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Dashtbin S, Razavi S, Ganjali Koli M, Barneh F, Ekhtiari-Sadegh S, Akbari R, Irajian G, Pooshang Bagheri K. Intracellular bactericidal activity and action mechanism of MDP1 antimicrobial peptide against VRSA and MRSA in human endothelial cells. Front Microbiol 2024; 15:1416995. [PMID: 39252832 PMCID: PMC11381295 DOI: 10.3389/fmicb.2024.1416995] [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: 04/13/2024] [Accepted: 08/05/2024] [Indexed: 09/11/2024] Open
Abstract
Introduction Staphylococcus aureus is a prominent cause of postoperative infections, often persisting within host cells, leading to chronic infections. Conventional antibiotics struggle to eliminate intracellular S. aureus due to poor cell penetration. Antimicrobial peptides are a new hope for tackling intracellular bacteria. Accordingly, this study examines the antimicrobial peptide MDP1, derived from melittin, for its efficacy against intracellular S. aureus. Methods In this study, the physiochemical properties (Prediction of three-dimensional structure, circular dichroism and helical wheel projection analysis) were investigated. Extracellular antibacterial activity and cytotoxicity of MDP1 were also assessed. The mechanism of interaction of MDP1 with S. aureus was evaluated by molecular dynamic simulation, atomic force and confocal microscopy. Bacterial internalization into an endothelial cell model was confirmed through culture and transmission electron microscopy. The effect of the peptide on intracellular bacteria was investigated by culture and epi-fluorescence microscopy. Results and discussion 3D structural prediction proved the conformation of MDP1 as an α-helix peptide. Helical-wheel projection analysis indicated the proper orientation of hydrophobic amino acid residues for membrane interaction. CD spectroscopy of MDP1 showed that MDP1 in SDS 10 and 30 mM adopted 87 and 91% helical conformation. Atomic force and confocal microscopy assessments as well as molecular dynamics studies revealed the peptide-bacterial membrane interaction. MDP1, at the concentration of 0.32 μg mL-1, demonstrated a fold reduction of 21.7 ± 1.8, 1.7 ± 0.2, and 7.3 ± 0.8 in intracellular bacterial load for ATCC, VRSA, and MRSA, respectively. Molecular dynamics results demonstrate a preferential interaction of MDP1 with POPG/POPE membranes, primarily driven by electrostatic forces and hydrogen bonding. In POPC systems, two out of four MDP1 interacted effectively, while all four MDP1 engaged with POPG/POPE membranes. Gathering all data together, MDP1 is efficacious in the reduction of intracellular VRSA and MRSA proved by culture and epi-fluorescent microscopy although further studies should be performed to increase the intracellular activity of MDP1.
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Affiliation(s)
- Shirin Dashtbin
- Microbial Biotechnology Research Center, Iran University of Medical Sciences, Tehran, Iran
- Department of Microbiology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Shabnam Razavi
- Microbial Biotechnology Research Center, Iran University of Medical Sciences, Tehran, Iran
- Department of Microbiology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mokhtar Ganjali Koli
- Department of Chemistry, University of Kurdistan, Sanandaj, Iran
- Computational Chemistry Laboratory, Kask Afrand Exire Ltd., Sanandaj, Iran
| | - Farnoosh Barneh
- Venom and Biotherapeutics Molecules Laboratory, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Sarvenaz Ekhtiari-Sadegh
- Venom and Biotherapeutics Molecules Laboratory, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Reza Akbari
- Department of Microbiology and Virology, School of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Gholamreza Irajian
- Microbial Biotechnology Research Center, Iran University of Medical Sciences, Tehran, Iran
- Department of Microbiology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Kamran Pooshang Bagheri
- Venom and Biotherapeutics Molecules Laboratory, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
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150
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Wang R, Tiwary P. Atomic scale insights into NaCl nucleation in nanoconfined environments. Chem Sci 2024:d4sc04042b. [PMID: 39234215 PMCID: PMC11367593 DOI: 10.1039/d4sc04042b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Accepted: 08/23/2024] [Indexed: 09/06/2024] Open
Abstract
In this work we examine the nucleation from NaCl aqueous solutions within nano-confined environments, employing enhanced sampling molecular dynamics simulations integrated with machine learning-derived reaction coordinates. Through our simulations, we successfully induce phase transitions between solid, liquid, and a hydrated phase, typically observed at lower temperatures in bulk environments. Interestingly, while generally speaking nano-confinement serves to stabilize the solid phase and elevate melting points, there are subtle variations in the thermodynamics of competing phases with the precise extent of confinement. Our simulations explain these findings by underscoring the significant role of water, alongside ion aggregation and subtle, anisotropic dielectric behavior, in driving nucleation within nano-confined environments. This report thus provides a framework for sampling, analyzing and understanding nucleation processes under nano-confinement.
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Affiliation(s)
- Ruiyu Wang
- Institute for Physical Science and Technology, University of Maryland College Park MD 20742 USA
| | - Pratyush Tiwary
- Institute for Physical Science and Technology, University of Maryland College Park MD 20742 USA
- Department of Chemistry and Biochemistry, University of Maryland College Park MD 20742 USA
- University of Maryland Institute for Health Computing Bethesda Maryland 20852 USA
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