1
|
Kubyshkin V, Rubini M. Proline Analogues. Chem Rev 2024; 124:8130-8232. [PMID: 38941181 DOI: 10.1021/acs.chemrev.4c00007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
Within the canonical repertoire of the amino acid involved in protein biogenesis, proline plays a unique role as an amino acid presenting a modified backbone rather than a side-chain. Chemical structures that mimic proline but introduce changes into its specific molecular features are defined as proline analogues. This review article summarizes the existing chemical, physicochemical, and biochemical knowledge about this peculiar family of structures. We group proline analogues from the following compounds: substituted prolines, unsaturated and fused structures, ring size homologues, heterocyclic, e.g., pseudoproline, and bridged proline-resembling structures. We overview (1) the occurrence of proline analogues in nature and their chemical synthesis, (2) physicochemical properties including ring conformation and cis/trans amide isomerization, (3) use in commercial drugs such as nirmatrelvir recently approved against COVID-19, (4) peptide and protein synthesis involving proline analogues, (5) specific opportunities created in peptide engineering, and (6) cases of protein engineering with the analogues. The review aims to provide a summary to anyone interested in using proline analogues in systems ranging from specific biochemical setups to complex biological systems.
Collapse
Affiliation(s)
| | - Marina Rubini
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
| |
Collapse
|
2
|
Hansen TN, Olsen CA. Contemporary Applications of Thioamides and Methods for Their Synthesis. Chemistry 2024; 30:e202303770. [PMID: 38088462 DOI: 10.1002/chem.202303770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Indexed: 12/23/2023]
Abstract
Thioamides are naturally occurring isosteres of amide bonds in which the chalcogen atom of the carbonyl is changed from oxygen to sulfur. This substitution gives rise to altered nucleophilicity and hydrogen bonding properties with importance for both chemical reactivity and non-covalent interactions. As such, thioamides have been introduced into biologically active compounds to achieve improved target affinity and/or stability towards hydrolytic enzymes but have also been applied as probes of protein and peptide folding and dynamics. Recently, a series of new methods have been developed for the synthesis of thioamides as well as their utilization in peptide chemistry. Further, novel strategies for the incorporation of thioamides into proteins have been developed, enabling both structural and functional studies to be performed. In this Review, we highlight the recent developments in the preparation of thioamides and their applications for peptide modification and study of protein function.
Collapse
Affiliation(s)
- Tobias N Hansen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, 2100, Copenhagen, Denmark
| | - Christian A Olsen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, 2100, Copenhagen, Denmark
| |
Collapse
|
3
|
Loughlin JO, Zinovjev K, Napolitano S, van der Kamp M, Rubini M. 4-Thiaproline accelerates the slow folding phase of proteins containing cis prolines in the native state by two orders of magnitude. Protein Sci 2024; 33:e4877. [PMID: 38115231 PMCID: PMC10804670 DOI: 10.1002/pro.4877] [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: 09/19/2023] [Revised: 12/12/2023] [Accepted: 12/14/2023] [Indexed: 12/21/2023]
Abstract
The cis/trans isomerization of peptidyl-prolyl peptide bonds is often the bottleneck of the refolding reaction for proteins containing cis proline residues in the native state. Proline (Pro) analogues, especially C4-substituted fluoroprolines, have been widely used in protein engineering to enhance the thermodynamic stability of peptides and proteins and to investigate folding kinetics. 4-thiaproline (Thp) has been shown to bias the ring pucker of Pro, to increase the cis population percentage of model peptides in comparison to Pro, and to diminish the activation energy barrier for the cis/trans isomerization reaction. Despite its intriguing properties, Thp has been seldom incorporated into proteins. Moreover, the impact of Thp on the folding kinetics of globular proteins has never been reported. In this study, we show that upon incorporation of Thp at cisPro76 into the thioredoxin variant Trx1P the half-life of the refolding reaction decreased from ~2 h to ~35 s. A dramatic acceleration of the refolding rate could be observed also for the protein pseudo wild-type barstar upon replacement of cisPro48 with Thp. Quantum chemical calculations suggested that the replacement of the Cγ H2 group by a sulfur atom in the pyrrolidine ring, might lower the barrier for cis/trans rotation due to a weakened peptide bond. The protein variants retained their thermodynamic stability upon incorporation of Thp, while the catalytic and enzymatic activities of the modified Trx1P remained unchanged. Our results show that the Pro isostere Thp might accelerate the rate of the slow refolding reaction for proteins containing cis proline residues in the native state, independent from the local structural environment.
Collapse
Affiliation(s)
| | - Kirill Zinovjev
- School of Biochemistry, University of BristolBristolUK
- Department of Physical ChemistryUniversity of ValenciaValenciaSpain
| | - Silvia Napolitano
- Department of Molecular Biology and BiophysicsETH ZürichZürichSwitzerland
| | | | - Marina Rubini
- School of Chemistry, University College Dublin, BelfieldDublin 4Ireland
| |
Collapse
|
4
|
Elena-Real CA, Mier P, Sibille N, Andrade-Navarro MA, Bernadó P. Structure-function relationships in protein homorepeats. Curr Opin Struct Biol 2023; 83:102726. [PMID: 37924569 DOI: 10.1016/j.sbi.2023.102726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 10/06/2023] [Accepted: 10/09/2023] [Indexed: 11/06/2023]
Abstract
Homorepeats (or polyX), protein segments containing repetitions of the same amino acid, are abundant in proteomes from all kingdoms of life and are involved in crucial biological functions as well as several neurodegenerative and developmental diseases. Mainly inserted in disordered segments of proteins, the structure/function relationships of homorepeats remain largely unexplored. In this review, we summarize present knowledge for the most abundant homorepeats, highlighting the role of the inherent structure and the conformational influence exerted by their flanking regions. Recent experimental and computational methods enable residue-specific investigations of these regions and promise novel structural and dynamic information for this elusive group of proteins. This information should increase our knowledge about the structural bases of phenomena such as liquid-liquid phase separation and trinucleotide repeat disorders.
Collapse
Affiliation(s)
- Carlos A Elena-Real
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS. 29 rue de Navacelles, 34090 Montpellier, France. https://twitter.com/carloselenareal
| | - Pablo Mier
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University Mainz. Hans-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany
| | - Nathalie Sibille
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS. 29 rue de Navacelles, 34090 Montpellier, France
| | - Miguel A Andrade-Navarro
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University Mainz. Hans-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany
| | - Pau Bernadó
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS. 29 rue de Navacelles, 34090 Montpellier, France.
| |
Collapse
|
5
|
Briceño-Vargas FM, Quesadas-Rojas M, Mirón-López G, Cáceres-Castillo D, Carballo RM, Mena-Rejón GJ, Quijano-Quiñones RF. Molecular orbital and topological electron density study of n → π* interactions: amides and thioamides cases. RSC Adv 2023; 13:31321-31329. [PMID: 37901275 PMCID: PMC10600513 DOI: 10.1039/d3ra06038a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 10/18/2023] [Indexed: 10/31/2023] Open
Abstract
The n → π* interactions were studied in amides and thioamides systems models, through the analysis of the electron density topology along with the Natural Bonding Orbital (NBO) approach. The effect of the dispersion terms was assessed using different DFT functionals. The NBO, independent gradient model (IGM), and the analysis of the reduced density gradient outcomes show that dispersion forces play a significant role in the strength of n → π* interactions. The IGM results indicate that δg height values for n → π* interactions do not extend beyond 0.025. All the methods used in this work predict that n → π* interaction between pairs of thioamides is stronger than those between amides. However, the electron density topology-based methods were not able to replicate the trends in the relative force of this interaction found in the experimental and NBO results.
Collapse
Affiliation(s)
- Flor María Briceño-Vargas
- Laboratory of Theoretical Chemistry, Faculty of Chemistry, Autonomous University of Yucatan Merida Yucatan 97069 Mexico
| | | | - Gumersindo Mirón-López
- Laboratory of Nuclear Magnetic Resonance, Faculty of Chemistry, Autonomous University of Yucatan Merida Yucatan 97069 Mexico
| | - David Cáceres-Castillo
- Laboratory of Pharmaceutical Chemistry, Faculty of Chemistry, Autonomous University of Yucatan Merida Yucatan 97069 Mexico
| | - Rubén M Carballo
- Laboratory of Pharmaceutical Chemistry, Faculty of Chemistry, Autonomous University of Yucatan Merida Yucatan 97069 Mexico
| | - Gonzalo J Mena-Rejón
- Laboratory of Pharmaceutical Chemistry, Faculty of Chemistry, Autonomous University of Yucatan Merida Yucatan 97069 Mexico
| | - Ramiro F Quijano-Quiñones
- Laboratory of Theoretical Chemistry, Faculty of Chemistry, Autonomous University of Yucatan Merida Yucatan 97069 Mexico
| |
Collapse
|
6
|
Li X, Hu L, Lu G, Wang Y. Carbon-Bonding Metal Catalysis (CBMC): A Supramolecular Complex Directs Structural-Isomer Selection in Gold-Catalyzed Reactions. J Am Chem Soc 2023; 145:21554-21561. [PMID: 37668596 DOI: 10.1021/jacs.3c07551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
Carbon is a primary element to constitute organic molecules, while metal catalysis is a basic tool in organic synthesis. The establishment of a link between the ubiquitous carbon bonding and metal catalysis is thus a fundamentally important problem. However, there is yet no experimental example to introduce the role of carbon bonding in a metal catalysis process. Herein, we merged the topics of carbon bonding and metal catalysis together and demonstrated that a supramolecular carbon-bonding metal complex can not only give rise to catalytic activity but, more remarkably, direct structural-isomer selection events in gold-catalyzed reactions. The experimental results unveil the fact that the imposing of weak carbon-bonding interactions on a gold complex can alter the carbene as well as the Lewis acid property of these catalysts. These results illustrate a non-negligible role of weak carbon-bonding interactions in the modulation of metal catalysis. As such, carbon-bonding metal catalysis is suggested to be used as a routine tool not only in the development of reactions but more frequently in analyzing reaction processes in metal catalysis.
Collapse
Affiliation(s)
- Xinxin Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Colloid and Interface Chemistry of the Ministry of Education, Shandong University, Jinan 250100, P. R. China
| | - Lingfei Hu
- School of Chemistry and Chemical Engineering, Key Laboratory of Colloid and Interface Chemistry of the Ministry of Education, Shandong University, Jinan 250100, P. R. China
| | - Gang Lu
- School of Chemistry and Chemical Engineering, Key Laboratory of Colloid and Interface Chemistry of the Ministry of Education, Shandong University, Jinan 250100, P. R. China
| | - Yao Wang
- School of Chemistry and Chemical Engineering, Key Laboratory of Colloid and Interface Chemistry of the Ministry of Education, Shandong University, Jinan 250100, P. R. China
| |
Collapse
|
7
|
Wang XD, Zhu J, Wang DX. Intermolecular n→π* Interactions in Supramolecular Chemistry and Catalysis. Chempluschem 2023; 88:e202300288. [PMID: 37609956 DOI: 10.1002/cplu.202300288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/19/2023] [Accepted: 08/21/2023] [Indexed: 08/24/2023]
Abstract
The n→π* interactions describing attractive force between lone pairs (lps) of nucleophile and carbonyl or polarized unsaturated bonds have recently attracted growing attentions in various disciplines. So far, such non-covalent driving force are mainly concentrated to intramolecular systems. Intermolecular n→π* interactions in principle could produce fascinated supramolecular systems or facilitate organic reactions, however, they remain largely underexplored due to the very weak energy of individual interaction. This review attempts to give an overview of the challenging intermolecular n→π* interactions, much efforts emphasize the supramolecular systems, catalytic processes and spectroscopic measurements.
Collapse
Affiliation(s)
- Xu-Dong Wang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Jun Zhu
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - De-Xian Wang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| |
Collapse
|
8
|
Rodríguez HA, Bickelhaupt FM, Fernández I. Origin of the Bürgi-Dunitz Angle. Chemphyschem 2023; 24:e202300379. [PMID: 37306022 DOI: 10.1002/cphc.202300379] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 06/09/2023] [Accepted: 06/12/2023] [Indexed: 06/13/2023]
Abstract
The Bürgi-Dunitz (BD) angle plays a pivotal role in organic chemistry to rationalize the nucleophilic addition to carbonyl groups. Yet, the origin of the obtuse trajectory of the nucleophile remains incompletely understood. Herein, we quantify the importance of the underlying physical factors quantum chemically. The obtuse BD angle appears to originate from the concerted action of a reduced Pauli repulsion between the nucleophile HOMO and carbonyl π bond, a more stabilizing HOMO-π*-LUMO(C=O) interaction, as well as a more favorable electrostatic attraction.
Collapse
Affiliation(s)
- Humberto A Rodríguez
- Departamento de Química Orgánica and Centro de Innovación en Química Avanzada (ORFEO-CINQA), Facultad de Ciencias Químicas, Universidad Complutense de Madrid Ciudad Universitaria, 28040-, Madrid, Spain
- Instituto de Productos Naturales y Agrobiología (IPNA), Consejo Superior de Investigaciones Científicas (CSIC), 38206-, La Laguna, Tenerife, Spain
| | - F Matthias Bickelhaupt
- Theoretical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, The Netherlands
- Institute for Molecules and Materials (IMM), Radboud University, Nijmegen, The Netherlands
- Department of Chemical Sciences, University of Johannesburg, South Africa
| | - Israel Fernández
- Departamento de Química Orgánica and Centro de Innovación en Química Avanzada (ORFEO-CINQA), Facultad de Ciencias Químicas, Universidad Complutense de Madrid Ciudad Universitaria, 28040-, Madrid, Spain
| |
Collapse
|
9
|
Banaś K, Lenartowicz P, Staś M, Dziuk B, Siodłak D. Insight into the Structure of Victorin, the Host-Selective Toxin from the Oat Pathogen Cochliobolus victoriae. Studies of the Unique Dehydroamino Acid β-Chlorodehydroalanine. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37486973 PMCID: PMC10401702 DOI: 10.1021/acs.jafc.3c01387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
Victorins, a family of peptide toxins, produced by the fungal pathogen Cochliobolus victoriae and responsible for disease of some oat varieties, contain a β-chlorodehydroalanine residue, ΔAla(βCl). To determine the conformational properties of this unique dehydroamino acid, a series of model compounds was studied using X-ray, NMR, and FT-IR methods, supported by theoretical calculations. The ΔAla(βCl) geometrical isomers differ in conformational profile. The isomer Z prefers the helical conformation α (φ, ψ = -61°, -24°), PPII type conformation β (φ, ψ = -47°, 136°), and semiextended conformation β2 (φ, ψ = -116°, 9°) in weakly and more polar solutions. The isomer E prefers mainly the extended conformation C5 (φ, ψ = -177°, 160°), but with an increase of the environment polarity also conformations β (φ, ψ = -44°, 132°) and α (φ, ψ = -53°, -39°). In the most stable conformations the N-H···Cl hydrogen bond (5γ) occurs, created between the chlorine atom of the side chain and the N-H donor of the flanking amide group. The method of synthesis of the β-chlorodehydroalanine residue is proposed, by chlorination of dehydroalanine and then the photoisomerization from the isomer Z to E. The presented results indicate that the assignment of the geometrical isomer of the ΔAla(βCl) residue in naturally occurring victorins still remains an open question, despite being crucial for biological activity.
Collapse
Affiliation(s)
- Karolina Banaś
- Faculty of Chemistry, University of Opole, Oleska 48, 45-052 Opole, Poland
| | - Paweł Lenartowicz
- Faculty of Chemistry, University of Opole, Oleska 48, 45-052 Opole, Poland
| | - Monika Staś
- Faculty of Chemistry, University of Opole, Oleska 48, 45-052 Opole, Poland
| | - Błażej Dziuk
- Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
- Faculty of Chemistry, University of Wroclaw, Joliot-Curie 14, Wroclaw 50-383, Poland
| | - Dawid Siodłak
- Faculty of Chemistry, University of Opole, Oleska 48, 45-052 Opole, Poland
| |
Collapse
|
10
|
Adhav V, Saikrishnan K. The Realm of Unconventional Noncovalent Interactions in Proteins: Their Significance in Structure and Function. ACS OMEGA 2023; 8:22268-22284. [PMID: 37396257 PMCID: PMC10308531 DOI: 10.1021/acsomega.3c00205] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 05/22/2023] [Indexed: 07/04/2023]
Abstract
Proteins and their assemblies are fundamental for living cells to function. Their complex three-dimensional architecture and its stability are attributed to the combined effect of various noncovalent interactions. It is critical to scrutinize these noncovalent interactions to understand their role in the energy landscape in folding, catalysis, and molecular recognition. This Review presents a comprehensive summary of unconventional noncovalent interactions, beyond conventional hydrogen bonds and hydrophobic interactions, which have gained prominence over the past decade. The noncovalent interactions discussed include low-barrier hydrogen bonds, C5 hydrogen bonds, C-H···π interactions, sulfur-mediated hydrogen bonds, n → π* interactions, London dispersion interactions, halogen bonds, chalcogen bonds, and tetrel bonds. This Review focuses on their chemical nature, interaction strength, and geometrical parameters obtained from X-ray crystallography, spectroscopy, bioinformatics, and computational chemistry. Also highlighted are their occurrence in proteins or their complexes and recent advances made toward understanding their role in biomolecular structure and function. Probing the chemical diversity of these interactions, we determined that the variable frequency of occurrence in proteins and the ability to synergize with one another are important not only for ab initio structure prediction but also to design proteins with new functionalities. A better understanding of these interactions will promote their utilization in designing and engineering ligands with potential therapeutic value.
Collapse
Affiliation(s)
- Vishal
Annasaheb Adhav
- Department of Biology, Indian Institute of Science Education and Research, Pune 411008, India
| | - Kayarat Saikrishnan
- Department of Biology, Indian Institute of Science Education and Research, Pune 411008, India
| |
Collapse
|
11
|
Watson PR, Gupta S, Hosseinzadeh P, Brown BP, Baker D, Christianson DW. Macrocyclic Octapeptide Binding and Inferences on Protein Substrate Binding to Histone Deacetylase 6. ACS Chem Biol 2023; 18:959-968. [PMID: 37027789 PMCID: PMC10130746 DOI: 10.1021/acschembio.3c00113] [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] [Indexed: 04/09/2023]
Abstract
Histone deacetylases (HDACs) are essential for the regulation of myriad biological processes, and their aberrant function is implicated in cancer, neurodegeneration, and other diseases. The cytosolic isozyme HDAC6 is unique among the greater family of deacetylases in that it contains two catalytic domains, CD1 and CD2. HDAC6 CD2 is responsible for tubulin deacetylase and tau deacetylase activities, inhibition of which is a key goal as new therapeutic approaches are explored. Of particular interest as HDAC inhibitors are naturally occurring cyclic tetrapeptides such as Trapoxin A or HC Toxin, or the cyclic depsipeptides Largazole and Romidepsin. Even more intriguing are larger, computationally designed macrocyclic peptide inhibitors. Here, we report the 2.0 Å resolution crystal structure of HDAC6 CD2 complexed with macrocyclic octapeptide 1. Comparison with the previously reported structure of the complex with macrocyclic octapeptide 2 reveals that a potent thiolate-zinc interaction made by the unnatural amino acid (S)-2-amino-7-sulfanylheptanoic acid contributes to nanomolar inhibitory potency for each inhibitor. Apart from this zinc-binding residue, octapeptides adopt strikingly different overall conformations and make few direct hydrogen bonds with the protein. Intermolecular interactions are dominated by water-mediated hydrogen bonds; in essence, water molecules appear to cushion the enzyme-octapeptide interface. In view of the broad specificity observed for protein substrates of HDAC6 CD2, we suggest that the binding of macrocyclic octapeptides may mimic certain features of the binding of macromolecular protein substrates.
Collapse
Affiliation(s)
- Paris R. Watson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104-6323, United States
| | - Suchetana Gupta
- Department of Bioengineering, Knight Campus, University of Oregon, Eugene, OR 97403 United States
| | - Parisa Hosseinzadeh
- Department of Bioengineering, Knight Campus, University of Oregon, Eugene, OR 97403 United States
| | - Benjamin P. Brown
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN 37235 United States
| | - David Baker
- Department of Biochemistry, Institute for Protein Design, University of Washington, Seattle, WA 98195 United States
| | - David W. Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104-6323, United States
| |
Collapse
|
12
|
Panwaria P, Das A. Effect of Substituents on the Intramolecular n→π* Interaction in 3-[2-(Dimethylamino) phenyl] propanal: A Computational Study. J Phys Chem A 2023; 127:3339-3346. [PMID: 37036493 DOI: 10.1021/acs.jpca.2c08641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
Abstract
n→π* non-covalent interaction (NCI) and hydrogen bond have similarity in terms of delocalization of the electron density between the two orbitals involved in the interaction. Hydrogen bond (X-H···Y) involves delocalization of the lone pair electrons (n) on the Y atom into the σ* orbital of the X-H bond. In contrast, the n→π* interaction deals with delocalizing the lone pair electrons (n) on the N, O, or S atom into the π* orbital of a C═O group or aromatic ring. Herein, we have shown a resemblance of this weak n→π* interaction with the relatively stronger hydrogen bond in terms of folding the side chains in flexible molecules. This work reports the study of folding of the flexible side-chain in 3-[2-(dimethylamino) phenyl] propanal (DMAPhP) through a N···C═O n→π* interaction using various computational approaches such as NBO, QTAIM, and NCI analyses. The folding of the molecule by the n→π* interaction observed in this study is found to be similar to that present in the secondary structures of peptides or proteins through hydrogen bonding interactions. Interestingly, the stabilization of the global minimum conformer of DMAPhP by the n→π* interaction demonstrates the importance of this NCI in providing conformational preferences in molecular systems. Another important finding of this study is that the theoretical redshift obtained in the C═O stretching frequency of the most stable conformer of the DMAPhP is contributed mostly by the n→π* interaction as the C═O group is not involved in hyperconjugation with any neighboring heteroatom, which is a common phenomenon in any ester or amide. We have also demonstrated here that the strength of the intramolecular n→π* interaction can be modulated by varying the electronic substituents at the para position of the donor group involved in the interaction.
Collapse
Affiliation(s)
- Prakash Panwaria
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Aloke Das
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| |
Collapse
|
13
|
Kojasoy V, Tantillo DJ. Importance of Noncovalent Interactions Involving Sulfur Atoms in Thiopeptide Antibiotics─Glycothiohexide α and Nocathiacin I. J Phys Chem A 2023; 127:2081-2090. [PMID: 36855831 DOI: 10.1021/acs.jpca.2c07600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Noncovalent interactions involving sulfur atoms play essential roles in protein structure and function by significantly contributing to protein stability, folding, and biological activity. Sulfur is a highly polarizable atom that can participate in many types of noncovalent interactions including hydrogen bonding, sulfur-π interactions, and S-lone pair interactions, but the impact of these sulfur-based interactions on molecular recognition and drug design is still often underappreciated. Here, we examine, using quantum chemical calculations, the roles of sulfur-based noncovalent interactions in complex naturally occurring molecules representative of thiopeptide antibiotics: glycothiohexide α and its close structural analogue nocathiacin I. While donor-acceptor orbital interactions make only very small contributions, electrostatic and dispersion contributions are predicted to be significant in many cases. In pursuit of understanding the magnitudes and nature of these noncovalent interactions, we made potential structural modifications that could significantly expand the chemical space of effective thiopeptide antibiotics.
Collapse
Affiliation(s)
- Volga Kojasoy
- Department of Chemistry, University of California─Davis, Davis, California 95616, United States
| | - Dean J Tantillo
- Department of Chemistry, University of California─Davis, Davis, California 95616, United States
| |
Collapse
|
14
|
Briand MA, Dreano L, Legehar A, Grazhdankin E, Ghemtio L, Xhaard H. Exploring cooperative molecular contacts using a PostgreSQL database system. Mol Inform 2023; 42:e2200235. [PMID: 36653303 DOI: 10.1002/minf.202200235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/30/2022] [Accepted: 01/18/2023] [Indexed: 01/20/2023]
Abstract
Cooperative molecular contacts play an important role in protein structure and ligand binding. Here, we constructed a PostgreSQL database that stores structural information in the form of atomic environments and allows flexible mining of molecular contacts. Taking the Ser-His-Asp/Glu catalytic triad as a first test case, we demonstrate that the presence of a carboxylate oxygen atom in the vicinity of a His is associated with shorter Ser-OH..N-His bond in the PDB30 subset. We prospectively mine catalytic triads in unannotated proteins, suggesting catalytic functions for unannotated proteins. As a second test case, we demonstrate that this database system can include ligand atoms, represented by Sybyl atom types, by evaluating the proportion of counter-ions for ligand carboxylate oxygens.
Collapse
Affiliation(s)
- Mael A Briand
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, FI-00014 University of Helsinki, P.O. Box 56 (Viikinkaari 5 E), Helsinki, Finland
| | - Loïc Dreano
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, FI-00014 University of Helsinki, P.O. Box 56 (Viikinkaari 5 E), Helsinki, Finland
| | - Ashenafi Legehar
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, FI-00014 University of Helsinki, P.O. Box 56 (Viikinkaari 5 E), Helsinki, Finland
| | - Evgeni Grazhdankin
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, FI-00014 University of Helsinki, P.O. Box 56 (Viikinkaari 5 E), Helsinki, Finland
| | - Léo Ghemtio
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, FI-00014 University of Helsinki, P.O. Box 56 (Viikinkaari 5 E), Helsinki, Finland
| | - Henri Xhaard
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, FI-00014 University of Helsinki, P.O. Box 56 (Viikinkaari 5 E), Helsinki, Finland
| |
Collapse
|
15
|
Kojasoy V, Tantillo DJ. Impacts of noncovalent interactions involving sulfur atoms on protein stability, structure, folding, and bioactivity. Org Biomol Chem 2022; 21:11-23. [PMID: 36345987 DOI: 10.1039/d2ob01602h] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
This review discusses the various types of noncovalent interactions in which sulfur atoms participate and their effects on protein stability, structure, folding and bioactivity. Current approaches and recommendations for modelling these noncovalent interactions (in terms of both geometries and interaction energies) are highlighted.
Collapse
Affiliation(s)
- Volga Kojasoy
- Department of Chemistry, University of California, Davis, 1 Shields Avenue, Davis, CA, 95616, USA.
| | - Dean J Tantillo
- Department of Chemistry, University of California, Davis, 1 Shields Avenue, Davis, CA, 95616, USA.
| |
Collapse
|
16
|
Dutta J, Routray C, Pandey S, Biswal HS. Intermolecular noncovalent interactions with carbon in solution. Chem Sci 2022; 13:14327-14335. [PMID: 36545132 PMCID: PMC9749111 DOI: 10.1039/d2sc05431k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/20/2022] [Indexed: 11/22/2022] Open
Abstract
One of the most familiar carbon-centered noncovalent interactions (NCIs) involving an antibonding π*-orbital situated at the Bürgi-Dunitz angle from the electron donor, mostly lone pairs of electrons, is known as n → π* interactions, and if it involves a σ* orbital in a linear fashion, then it is known as the carbon bond. These NCIs can be intra- or inter-molecular and are usually weak in strength but have a paramount effect on the structure and function of small-molecular crystals and proteins. Surprisingly, the experimental evidence of such interactions in the solution phase is scarce. It is even difficult to determine the interaction energy in the solution. Using NMR spectroscopy aided with molecular dynamics (MD) simulation and high-level quantum mechanical calculations, herein we provide the experimental evidence of intermolecular carbon-centered NCIs in solution. The challenge was to find appropriate heterodimers that could sustain room temperature thermal energy and collisions from the solvent molecules. However, after several trial model compounds, the pyridine-N-oxide:dimethyltetracyanocyclopropane (PNO-DMTCCP) complex was found to be a good candidate for the investigation. NBO analyses show that the PNO:DMTCCP complex is stabilized mainly by intermolecular n → π* interaction when a weaker carbon bond gives extra stability to the complex. From the NMR study, it is observed that the NCIs between DMTCCP and PNO are enthalpy driven with an enthalpy change of -28.12 kJ mol-1 and dimerization energy of ∼-38 kJ mol-1 is comparable to the binding energies of a conventional hydrogen-bonded dimer. This study opens up a new strategy to investigate weak intermolecular interactions such as n → π* interaction and carbon bonds in the solution phase.
Collapse
Affiliation(s)
- Juhi Dutta
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) PO - Bhimpur-Padanpur, Via-Jatni, District - Khurda PIN - 752050 Bhubaneswar India +91-674-2494-185, +91-674-2494-186
- Homi Bhabha National Institute, Training School Complex Anushakti Nagar Mumbai 400094 India
| | - Chinmay Routray
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) PO - Bhimpur-Padanpur, Via-Jatni, District - Khurda PIN - 752050 Bhubaneswar India +91-674-2494-185, +91-674-2494-186
- Homi Bhabha National Institute, Training School Complex Anushakti Nagar Mumbai 400094 India
| | - Shalini Pandey
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) PO - Bhimpur-Padanpur, Via-Jatni, District - Khurda PIN - 752050 Bhubaneswar India +91-674-2494-185, +91-674-2494-186
- Homi Bhabha National Institute, Training School Complex Anushakti Nagar Mumbai 400094 India
| | - Himansu S Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) PO - Bhimpur-Padanpur, Via-Jatni, District - Khurda PIN - 752050 Bhubaneswar India +91-674-2494-185, +91-674-2494-186
- Homi Bhabha National Institute, Training School Complex Anushakti Nagar Mumbai 400094 India
| |
Collapse
|
17
|
Livingstone K, Siebold K, Meyer S, Martín-Heras V, Daniliuc CG, Gilmour R. Skeletal Ring Contractions via I(I)/I(III) Catalysis: Stereoselective Synthesis of cis-α,α-Difluorocyclopropanes. ACS Catal 2022; 12:14507-14516. [PMID: 36504915 PMCID: PMC9724094 DOI: 10.1021/acscatal.2c04511] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/17/2022] [Indexed: 11/12/2022]
Abstract
The clinical success of α,α-difluorocyclopropanes, combined with limitations in the existing synthesis portfolio, inspired the development of an operationally simple, organocatalysis-based strategy to access cis-configured derivatives with high levels of stereoselectivity (up to >20:1 cis:trans). Leveraging an I(I)/I(III)-catalysis platform in the presence of an inexpensive HF source, it has been possible to exploit disubstituted bicyclobutanes (BCBs) as masked cyclobutene equivalents for this purpose. In situ generation of this strained alkene, enabled by Brønsted acid activation, facilitates an unprecedented 4 → 3 fluorinative ring contraction, to furnish cis-α,α-difluorinated cyclopropanes in a highly stereoselective manner (up to 88% yield). Mechanistic studies are disclosed together with conformational analysis (X-ray crystallography and NMR) to validate cis-α,α-difluorocyclopropanes as isosteres of the 1,4-dicarbonyl moiety. Given the importance of this unit in biology and the foundational no → π* interactions that manifest themselves in this conformation (e.g., collagen), it is envisaged that the title motif will find application in focused molecular design.
Collapse
|
18
|
Kashif Khan R, Meanwell NA, Hager HH. Pseudoprolines as stereoelectronically tunable proline isosteres. Bioorg Med Chem Lett 2022; 75:128983. [PMID: 36096342 DOI: 10.1016/j.bmcl.2022.128983] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/29/2022] [Accepted: 09/05/2022] [Indexed: 11/18/2022]
Abstract
The cyclic structure of proline (Pro) confers unique conformational properties on this natural amino acid that influences polypeptide structure and function. Pseudoprolines are a family of Pro isosteres that incorporate a heteroatom, most prominently oxygen or sulfur but also silicon and selenium, to replace the Cβ or Cγ carbon atom of the pyrrolidine ring. These readily synthetically accessible structural motifs can facilitate facile molecular editing in a fashion that allows modulation of the amide bond topology of dipeptide elements and influence over ring pucker. While the properties of pseudoprolines have been exploited most prominently in the design of oligopeptide analogues, they have potential application in the design and optimization of small molecules. In this Digest, we summarize the physicochemical properties of pseudoprolines and illustrate their potential in drug discovery by surveying examples of applications in the design of bioactive molecules.
Collapse
Affiliation(s)
- R Kashif Khan
- Small Molecule Drug Discovery, Bristol Myers Squibb Research and Early Development, 100 Binney Street, Cambridge, MA 02142, USA.
| | - Nicholas A Meanwell
- Small Molecule Drug Discovery, Bristol Myers Squibb Research and Early Development, P.O. Box 4000, Princeton, NJ 08543-4000, USA.
| | - Harry H Hager
- Small Molecule Drug Discovery, Bristol Myers Squibb Research and Early Development, 200 Cambridgepark Drive, Cambridge, MA 02140, USA.
| |
Collapse
|
19
|
Diehl CJ, Ciulli A. Discovery of small molecule ligands for the von Hippel-Lindau (VHL) E3 ligase and their use as inhibitors and PROTAC degraders. Chem Soc Rev 2022; 51:8216-8257. [PMID: 35983982 PMCID: PMC9528729 DOI: 10.1039/d2cs00387b] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The von Hippel-Lindau (VHL) Cullin RING E3 ligase is an essential enzyme in the ubiquitin-proteasome system that recruits substrates such as the hypoxia inducible factor for ubiquitination and subsequent proteasomal degradation. The ubiquitin-proteasome pathway can be hijacked toward non-native neo-substrate proteins using proteolysis targeting chimeras (PROTACs), bifunctional molecules designed to simultaneously bind to an E3 ligase and a target protein to induce target ubiquitination and degradation. The availability of high-quality small-molecule ligands with good binding affinity for E3 ligases is fundamental for PROTAC development. Lack of good E3 ligase ligands as starting points to develop PROTAC degraders was initially a stumbling block to the development of the field. Herein, the journey towards the design of small-molecule ligands binding to VHL is presented. We cover the structure-based design of VHL ligands, their application as inhibitors in their own right, and their implementation into rationally designed, potent PROTAC degraders of various target proteins. We highlight the key findings and learnings that have provided strong foundations for the remarkable development of targeted protein degradation, and that offer a blueprint for designing new ligands for E3 ligases beyond VHL.
Collapse
Affiliation(s)
- Claudia J Diehl
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, Scotland, UK.
| | - Alessio Ciulli
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, Scotland, UK.
| |
Collapse
|
20
|
Fiala T, Barros EP, Ebert MO, Ruijsenaars E, Riniker S, Wennemers H. Frame Shifts Affect the Stability of Collagen Triple Helices. J Am Chem Soc 2022; 144:18642-18649. [PMID: 36179150 DOI: 10.1021/jacs.2c08727] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Collagen model peptides (CMPs), composed of proline-(2S,4R)-hydroxyproline-glycine (POG) repeat units, have been extensively used to study the structure and stability of triple-helical collagen─the dominant structural protein in mammals─at the molecular level. Despite the more than 50-year history of CMPs and numerous studies on the relationship between the composition of single-stranded CMPs and the thermal stability of the assembled triple helices, little attention has been paid to the effects arising from their terminal residues. Here, we show that frame-shifted CMPs, which share POG repeat units but terminate with P, O, or G, form triple helices with vastly different thermal stabilities. A melting temperature difference as high as 16 °C was found for triple helices from 20-mers Ac-OG[POG]6-NH2 and Ac-[POG]6PO-NH2, and triple helices of the constitutional isomers Ac-[POG]7-NH2 and Ac-[GPO]7-NH2 melt 10 °C apart. A combination of thermal denaturation, circular dichroism and NMR spectroscopic studies, and molecular dynamics simulations revealed that the stability differences originate from the propensity of the peptide termini to preorganize into a polyproline-II helical structure. Our results advise that care must be taken when designing peptide mimics of structural proteins, as subtle changes in the terminal residues can significantly affect their properties. Our findings also provide a general and straightforward tool for tuning the stability of CMPs for applications as synthetic materials and biological probes.
Collapse
Affiliation(s)
- Tomas Fiala
- Laboratory of Organic Chemistry, ETH Zurich, D-CHAB, Vladimir-Prelog-Weg 3, Zurich 8093, Switzerland
| | - Emilia P Barros
- Laboratory of Physical Chemistry, ETH Zurich, D-CHAB, Vladimir-Prelog-Weg 2, Zurich 8093, Switzerland
| | - Marc-Olivier Ebert
- Laboratory of Organic Chemistry, ETH Zurich, D-CHAB, Vladimir-Prelog-Weg 3, Zurich 8093, Switzerland
| | - Enrico Ruijsenaars
- Laboratory of Physical Chemistry, ETH Zurich, D-CHAB, Vladimir-Prelog-Weg 2, Zurich 8093, Switzerland
| | - Sereina Riniker
- Laboratory of Physical Chemistry, ETH Zurich, D-CHAB, Vladimir-Prelog-Weg 2, Zurich 8093, Switzerland
| | - Helma Wennemers
- Laboratory of Organic Chemistry, ETH Zurich, D-CHAB, Vladimir-Prelog-Weg 3, Zurich 8093, Switzerland
| |
Collapse
|
21
|
Purushotham M, Paul B, Govindachar DM, Singh AK, Periyasamy G, Peter SC. Ortho-halogen effects: n→π* interactions, halogen bonding, and deciphering chiral attributes in N-aryl glycine peptoid foldamers. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133276] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
22
|
Intrinsically fluorescent polyureas toward conformation-assisted metamorphosis, discoloration and intracellular drug delivery. Nat Commun 2022; 13:4551. [PMID: 35931687 PMCID: PMC9355952 DOI: 10.1038/s41467-022-32053-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 07/13/2022] [Indexed: 11/08/2022] Open
Abstract
Peptidomimetic polymers have attracted increasing interest because of the advantages of facile synthesis, high molecular tunability, resistance to degradation, and low immunogenicity. However, the presence of non-native linkages compromises their ability to form higher ordered structures and protein-inspired functions. Here we report a class of amino acid-constructed polyureas with molecular weight- and solvent-dependent helical and sheet-like conformations as well as green fluorescent protein-mimic autofluorescence with aggregation-induced emission characteristics. The copolymers self-assemble into vesicles and nanotubes and exhibit H-bonding-mediated metamorphosis and discoloration behaviors. We show that these polymeric vehicles with ultrahigh stability, superfast responsivity and conformation-assisted cell internalization efficiency could act as an “on-off” switchable nanocarrier for specific intracellular drug delivery and effective cancer theranosis in vitro and in vivo. This work provides insights into the folding and hierarchical assembly of biomacromolecules, and a new generation of bioresponsive polymers and nonconventional luminescent aliphatic materials for diverse applications. Biomimetic materials are of interest but can often suffer from limitations caused by the non-native linkages used. Here, the authors report on the creation of amino acid constructed polyureas which can self-assemble into vesicles and nanotubes with aggregation induced fluorescence and the potential for drug delivery applications.
Collapse
|
23
|
Meredith NY, Borsley S, Smolyar IV, Nichol GS, Baker CM, Ling KB, Cockroft SL. Dissecting Solvent Effects on Hydrogen Bonding. Angew Chem Int Ed Engl 2022; 61:e202206604. [PMID: 35608961 PMCID: PMC9400978 DOI: 10.1002/anie.202206604] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Indexed: 12/26/2022]
Abstract
The experimental isolation of H-bond energetics from the typically dominant influence of the solvent remains challenging. Here we use synthetic molecular balances to quantify amine/amide H-bonds in competitive solvents. Over 200 conformational free energy differences were determined using 24 H-bonding balances in 9 solvents spanning a wide polarity range. The correlations between experimental interaction energies and gas-phase computed energies exhibited wild solvent-dependent variation. However, excellent correlations were found between the same computed energies and the experimental data following empirical dissection of solvent effects using Hunter's α/β solvation model. In addition to facilitating the direct comparison of experimental and computational data, changes in the fitted donor and acceptor constants reveal the energetics of secondary local interactions such as competing H-bonds.
Collapse
Affiliation(s)
- Nicole Y. Meredith
- EaStCHEM School of ChemistryUniversity of EdinburghJoseph Black Building, David Brewster RoadEdinburghEH9 3FJUK
| | - Stefan Borsley
- EaStCHEM School of ChemistryUniversity of EdinburghJoseph Black Building, David Brewster RoadEdinburghEH9 3FJUK
| | - Ivan V. Smolyar
- EaStCHEM School of ChemistryUniversity of EdinburghJoseph Black Building, David Brewster RoadEdinburghEH9 3FJUK
| | - Gary S. Nichol
- EaStCHEM School of ChemistryUniversity of EdinburghJoseph Black Building, David Brewster RoadEdinburghEH9 3FJUK
| | - Christopher M. Baker
- SyngentaJealott's Hill International Research CentreBracknell, BerkshireRG42 6EYUK
| | - Kenneth B. Ling
- SyngentaJealott's Hill International Research CentreBracknell, BerkshireRG42 6EYUK
| | - Scott L. Cockroft
- EaStCHEM School of ChemistryUniversity of EdinburghJoseph Black Building, David Brewster RoadEdinburghEH9 3FJUK
| |
Collapse
|
24
|
Panwaria P, Das A. Understanding the n → π* non-covalent interaction using different experimental and theoretical approaches. Phys Chem Chem Phys 2022; 24:22371-22389. [PMID: 35822956 DOI: 10.1039/d2cp02070j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein, a perspective on the recent understanding of weak n → π* interaction obtained using different experimental and theoretical approaches is presented. This interaction is purely an orbital interaction that involves the delocalization of the lone pair electrons (n) on nitrogen, oxygen, and sulfur to the π* orbitals of CO, CN, and aromatic rings. The n → π* interaction has been found to profoundly influence the stabilization of peptides, proteins, drugs, and various small molecules. Although the functional properties of this non-covalent interaction are still quite underestimated, there are recent demonstrations of applying this interaction to the regulation of synthetic chemistry, catalysis, and molecular recognition. However, the identification and quantification of the n → π* interaction remain a demanding task as this interaction is quite weak and based on the electron delocalization between the two orbitals, while hyperconjugation interactions between neighboring atoms and the group involved in the n → π* interaction are simultaneously present. This review provides a comprehensive picture of understanding the n → π* interaction using different experimental approaches such as the X-ray diffraction technique, and electronic, NMR, microwave, and IR spectroscopy, in addition to quantum chemistry calculations. A detailed understanding of the n → π* interaction can help in modulating the strength of this interaction, which will be further helpful in designing efficient drugs, synthetic peptides, peptidomimetics, etc.
Collapse
Affiliation(s)
- Prakash Panwaria
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr. Homi Bhabha Road, Pashan, Pune-411008, India.
| | - Aloke Das
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr. Homi Bhabha Road, Pashan, Pune-411008, India.
| |
Collapse
|
25
|
Santos JL, Janegitz BC, de Oliveira MR, de Souza GL. Exploring the water hydrogen-bonding effects on the ground and low-lying excited states of serotonin. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
26
|
Meredith NY, Borsley S, Smolyar IV, Nichol GS, Baker CM, Ling KB, Cockroft SL. Dissecting Solvent Effects on Hydrogen Bonding. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202206604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Nicole Y. Meredith
- EaStCHEM School of Chemistry University of Edinburgh Joseph Black Building, David Brewster Road Edinburgh EH9 3FJ UK
| | - Stefan Borsley
- EaStCHEM School of Chemistry University of Edinburgh Joseph Black Building, David Brewster Road Edinburgh EH9 3FJ UK
| | - Ivan V. Smolyar
- EaStCHEM School of Chemistry University of Edinburgh Joseph Black Building, David Brewster Road Edinburgh EH9 3FJ UK
| | - Gary S. Nichol
- EaStCHEM School of Chemistry University of Edinburgh Joseph Black Building, David Brewster Road Edinburgh EH9 3FJ UK
| | - Christopher M. Baker
- Syngenta Jealott's Hill International Research Centre Bracknell, Berkshire RG42 6EY UK
| | - Kenneth B. Ling
- Syngenta Jealott's Hill International Research Centre Bracknell, Berkshire RG42 6EY UK
| | - Scott L. Cockroft
- EaStCHEM School of Chemistry University of Edinburgh Joseph Black Building, David Brewster Road Edinburgh EH9 3FJ UK
| |
Collapse
|
27
|
Mitra D, Das Mohapatra PK. In silico comparative structural and compositional analysis of glycoproteins of RSV to study the nature of stability and transmissibility of RSV A. SYSTEMS MICROBIOLOGY AND BIOMANUFACTURING 2022; 3:312-327. [PMID: 38013803 PMCID: PMC9135598 DOI: 10.1007/s43393-022-00110-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/07/2022] [Accepted: 05/08/2022] [Indexed: 11/29/2022]
Abstract
The current scenario of COVID-19 makes us to think about the devastating diseases that kill so many people every year. Analysis of viral proteins contributes many things that are utterly useful in the evolution of therapeutic drugs and vaccines. In this study, sequence and structure of fusion glycoproteins and major surface glycoproteins of respiratory syncytial virus (RSV) were analysed to reveal the stability and transmission rate. RSV A has the highest abundance of aromatic residues. The Kyte-Doolittle scale indicates the hydrophilic nature of RSV A protein which leads to the higher transmission rate of this virus. Intra-protein interactions such as carbonyl interactions, cation-pi, and salt bridges were shown to be greater in RSV A compared to RSV B, which might lead to improved stability. This study discovered the presence of a network aromatic-sulphur interaction in viral proteins. Analysis of ligand binding pocket of RSV proteins indicated that drugs are performing better on RSV B than RSV A. It was also shown that increasing the number of tunnels in RSV A proteins boosts catalytic activity. This study will be helpful in drug discovery and vaccine development.
Collapse
Affiliation(s)
- Debanjan Mitra
- Department of Microbiology, Raiganj University, Raiganj, WB India
| | | |
Collapse
|
28
|
Jena S, Dutta J, Tulsiyan KD, Sahu AK, Choudhury SS, Biswal HS. Noncovalent interactions in proteins and nucleic acids: beyond hydrogen bonding and π-stacking. Chem Soc Rev 2022; 51:4261-4286. [PMID: 35560317 DOI: 10.1039/d2cs00133k] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Understanding the noncovalent interactions (NCIs) among the residues of proteins and nucleic acids, and between drugs and proteins/nucleic acids, etc., has extraordinary relevance in biomolecular structure and function. It helps in interpreting the dynamics of complex biological systems and enzymatic activity, which is esential for new drug design and efficient drug delivery. NCIs like hydrogen bonding (H-bonding) and π-stacking have been researchers' delight for a long time. Prominent among the recently discovered NCIs are halogen, chalcogen, pnictogen, tetrel, carbo-hydrogen, and spodium bonding, and n → π* interaction. These NCIs have caught the imaginations of various research groups in recent years while explaining several chemical and biological processes. At this stage, a holistic view of these new ideas and findings lying scattered can undoubtedly trigger our minds to explore more. The present review attempts to address NCIs beyond H-bonding and π-stacking, which are mainly n → σ*, n → π* and σ → σ* type interactions. Five of the seven NCIs mentioned earlier are linked to five non-inert end groups of the modern periodic table. Halogen (group-17) bonding is one of the oldest and most explored NCIs, which finds its relevance in biomolecules due to the phase correction and inhibitory properties of halogens. Chalcogen (group 16) bonding serves as a redox-active functional group of different active sites of enzymes and acts as a nucleophile in proteases and phosphates. Pnictogen (group 15), tetrel (group 14), triel (group 13) and spodium (group 12) bonding does exist in biomolecules. The n → π* interactions are linked to backbone carbonyl groups and protein side chains. Thus, they are crucial in determining the conformational stability of the secondary structures in proteins. In addition, a more recently discovered to and fro σ → σ* type interaction, namely carbo-hydrogen bonding, is also present in protein-ligand systems. This review summarizes these grand epiphanies routinely used to elucidate the structure and dynamics of biomolecules, their enzymatic activities, and their application in drug discovery. It also briefs about the future perspectives and challenges posed to the spectroscopists and theoreticians.
Collapse
Affiliation(s)
- Subhrakant Jena
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
| | - Juhi Dutta
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
| | - Kiran Devi Tulsiyan
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
| | - Akshay Kumar Sahu
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
| | - Shubhranshu Shekhar Choudhury
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
| | - Himansu S Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
| |
Collapse
|
29
|
Zhang Q, Crespi S, Toyoda R, Costil R, Browne WR, Qu DH, Tian H, Feringa BL. Stereodivergent Chirality Transfer by Noncovalent Control of Disulfide Bonds. J Am Chem Soc 2022; 144:4376-4382. [PMID: 35120292 PMCID: PMC8931715 DOI: 10.1021/jacs.1c10000] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
Controlling dynamic
stereochemistry is an important challenge,
as it is not only inherent to protein structure and function but often
governs supramolecular systems and self-assembly. Typically, disulfide
bonds exhibit stereodivergent behavior in proteins; however, how chiral
information is transmitted to disulfide bonds remains unclear. Here,
we report that hydrogen bonds are essential in the control of disulfide
chirality and enable stereodivergent chirality transfer. The formation
of S–S···H–N hydrogen bonds in solution
can drive conformational adaption to allow intramolecular chirality
transfer, while the formation of C=O···H–N hydrogen
bonds results in supramolecular chirality transfer to form antiparallel
helically self-assembled solid-state architectures. The dependence
on the structural information encoded in the homochiral amino acid
building blocks reveals the remarkable dynamic stereochemical space
accessible through noncovalent chirality transmission.
Collapse
Affiliation(s)
- Qi Zhang
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China.,Stratingh Institute for Chemistry and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Stefano Crespi
- Stratingh Institute for Chemistry and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Ryojun Toyoda
- Stratingh Institute for Chemistry and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Romain Costil
- Stratingh Institute for Chemistry and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Wesley R Browne
- Stratingh Institute for Chemistry and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Da-Hui Qu
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - He Tian
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Ben L Feringa
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China.,Stratingh Institute for Chemistry and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| |
Collapse
|
30
|
Neveselý T, Molloy JJ, McLaughlin C, Brüss L, Daniliuc CG, Gilmour R. Leveraging the n→π* Interaction in Alkene Isomerization by Selective Energy Transfer Catalysis. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202113600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Tomáš Neveselý
- Organisch-Chemisches Institut Westfälische Wilhelms-Universität Münster Corrensstrasse 36 48149 Münster Germany
| | - John J. Molloy
- Organisch-Chemisches Institut Westfälische Wilhelms-Universität Münster Corrensstrasse 36 48149 Münster Germany
- Current address: Max Planck Institute of Colloids and Interfaces Am Mühlenberg 1 14476 Potsdam Germany
| | - Calum McLaughlin
- Organisch-Chemisches Institut Westfälische Wilhelms-Universität Münster Corrensstrasse 36 48149 Münster Germany
| | - Linda Brüss
- Organisch-Chemisches Institut Westfälische Wilhelms-Universität Münster Corrensstrasse 36 48149 Münster Germany
| | - Constantin G. Daniliuc
- Organisch-Chemisches Institut Westfälische Wilhelms-Universität Münster Corrensstrasse 36 48149 Münster Germany
| | - Ryan Gilmour
- Organisch-Chemisches Institut Westfälische Wilhelms-Universität Münster Corrensstrasse 36 48149 Münster Germany
| |
Collapse
|
31
|
Neveselý T, Molloy JJ, McLaughlin C, Brüss L, Daniliuc CG, Gilmour R. Leveraging the n→π* Interaction in Alkene Isomerization by Selective Energy Transfer Catalysis. Angew Chem Int Ed Engl 2022; 61:e202113600. [PMID: 34748684 PMCID: PMC9299456 DOI: 10.1002/anie.202113600] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Indexed: 11/09/2022]
Abstract
Examples of geometric alkene isomerization in nature are often limited to the net exergonic direction (ΔG°<0), with the antipodal net endergonic processes (ΔG°>0) comparatively under-represented. Inspired by the expansiveness of the maleate to fumarate (Z→E) isomerization in biochemistry, we investigated the inverse E→Z variant to validate nO →πC=O * interactions as a driving force for contra-thermodynamic isomerization. A general protocol involving selective energy transfer catalysis with inexpensive thioxanthone as a sensitizer (λmax =402 nm) is disclosed. Whilst in the enzymatic process nO →πC=O * interactions commonly manifest themselves in the substrate, these same interactions are shown to underpin directionality in the antipodal reaction by shortening the product alkene chromophore. The process was validated with diverse fumarate derivatives (>30 examples, up to Z:E>99:1), including the first examples of tetrasubstituted alkenes, and the involvement of nO →πC=O * interactions was confirmed by X-ray crystallography.
Collapse
Affiliation(s)
- Tomáš Neveselý
- Organisch-Chemisches InstitutWestfälische Wilhelms-Universität MünsterCorrensstrasse 3648149MünsterGermany
| | - John J. Molloy
- Organisch-Chemisches InstitutWestfälische Wilhelms-Universität MünsterCorrensstrasse 3648149MünsterGermany
- Current address: Max Planck Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
| | - Calum McLaughlin
- Organisch-Chemisches InstitutWestfälische Wilhelms-Universität MünsterCorrensstrasse 3648149MünsterGermany
| | - Linda Brüss
- Organisch-Chemisches InstitutWestfälische Wilhelms-Universität MünsterCorrensstrasse 3648149MünsterGermany
| | - Constantin G. Daniliuc
- Organisch-Chemisches InstitutWestfälische Wilhelms-Universität MünsterCorrensstrasse 3648149MünsterGermany
| | - Ryan Gilmour
- Organisch-Chemisches InstitutWestfälische Wilhelms-Universität MünsterCorrensstrasse 3648149MünsterGermany
| |
Collapse
|
32
|
Zhang X, Yang J, Zhao J. Ynamide-Mediated Synthetic Approach to Thioamide-Substituted Peptides. Methods Mol Biol 2022; 2530:69-80. [PMID: 35761043 DOI: 10.1007/978-1-0716-2489-0_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A novel synthetic approach to thioamide-substituted peptides is reported. It provides a practical tool for the chemical biology study of peptides and proteins by replacing a carbonyl oxygen atom of an amide bond by an sp2-hybridized sulfur atom to precisely introduce a thioamide bond Ψ[CS-NH] into a peptide backbone. The α-thioacyloxyenamide intermediates, originating from ynamide coupling reagent and proteinogenic amino monothioacids, are proved to be novel effective thioacylating reagents in both the solution and solid phase peptide syntheses. Herein, we describe the detailed synthesis protocol for site-specifically incorporating a thioamide bond at 19 of 20 proteinogenic amino acid residues (except for His) of a peptide backbone in a racemization/epimerization-free manner.
Collapse
Affiliation(s)
- Xue Zhang
- School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, Shaanxi, China
| | - Jinhua Yang
- School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, Shaanxi, China
| | - Junfeng Zhao
- School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, Shaanxi, China.
- School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou, China.
| |
Collapse
|
33
|
Arcoria PJ, Ware RI, Makwana SV, Troya D, Etzkorn FA. Conformational Analysis of Fluoro-, Chloro-, and Proteo-Alkene Gly-Pro and Pro-Pro Isosteres to Mimic Collagen. J Phys Chem B 2021; 126:217-228. [PMID: 34968406 DOI: 10.1021/acs.jpcb.1c09180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Collagen is the most abundant human protein, with the canonical sequence (Gly-Pro-Hyp)n in its triple helix region. Cis-trans isomerization of the Xaa-Pro amide has made two of these amide bonds the target of alkene replacement: the Gly-Pro and the Pro-Hyp positions. The conformations of Gly-Pro and Pro-Pro (as a Pro-Hyp model) fluoro-, chloro-, and proteo-alkene mimic models were investigated computationally to determine whether these alkenes can stabilize the polyproline type II (PPII) conformation of collagen. Second-order Møller-Plesset (MP2) calculations with various basis sets were used to perform the conformational analyses and locate stationary points. The calculation results predict that fluoro- and chloro-alkene mimics of Gly-Pro and Pro-Pro can participate in n→π* donation to stabilize PPII conformations, yet they are poor n→π* acceptors, shifting the global minima away from PPII conformations. For the proteo-alkene mimics, the lack of significant n→π* interactions and unstable PPII-like geometries explains their known destabilization of the triple helix in collagen-like peptides.
Collapse
Affiliation(s)
- Paul J Arcoria
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Rachel I Ware
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Sunny V Makwana
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Diego Troya
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Felicia A Etzkorn
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| |
Collapse
|
34
|
Lampkin BJ, VanVeller B. Hydrogen Bond and Geometry Effects of Thioamide Backbone Modifications. J Org Chem 2021; 86:18287-18291. [PMID: 34851645 DOI: 10.1021/acs.joc.1c02373] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Thioamide substitution of backbone peptide bonds can probe interactions along the main chain of proteins. Despite theoretical predictions of the enhanced hydrogen bonding propensities of thioamides, previous studies often do not consider the geometric constraints imposed by folded peptide secondary structure. This work addresses drawbacks in previous studies that ignored the geometry dependence and local dielectric properties of thioamide hydrogen bonding and identifies cases where thioamides may be either stronger or weaker hydrogen-bonding partners than amides.
Collapse
Affiliation(s)
- Bryan J Lampkin
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Brett VanVeller
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| |
Collapse
|
35
|
Mardirossian M, Rubini M, Adamo MFA, Scocchi M, Saviano M, Tossi A, Gennaro R, Caporale A. Natural and Synthetic Halogenated Amino Acids-Structural and Bioactive Features in Antimicrobial Peptides and Peptidomimetics. Molecules 2021; 26:7401. [PMID: 34885985 PMCID: PMC8659048 DOI: 10.3390/molecules26237401] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 11/16/2021] [Accepted: 11/26/2021] [Indexed: 11/17/2022] Open
Abstract
The 3D structure and surface characteristics of proteins and peptides are crucial for interactions with receptors or ligands and can be modified to some extent to modulate their biological roles and pharmacological activities. The introduction of halogen atoms on the side-chains of amino acids is a powerful tool for effecting this type of tuning, influencing both the physico-chemical and structural properties of the modified polypeptides, helping to first dissect and then rationally modify features that affect their mode of action. This review provides examples of the influence of different types of halogenation in amino acids that replace native residues in proteins and peptides. Examples of synthetic strategies for obtaining halogenated amino acids are also provided, focusing on some representative compounds and their biological effects. The role of halogenation in native and designed antimicrobial peptides (AMPs) and their mimetics is then discussed. These are in the spotlight for the development of new antimicrobial drugs to counter the rise of antibiotic-resistant pathogens. AMPs represent an interesting model to study the role that natural halogenation has on their mode of action and also to understand how artificially halogenated residues can be used to rationally modify and optimize AMPs for pharmaceutical purposes.
Collapse
Affiliation(s)
- Mario Mardirossian
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Piazza dell’Ospitale, 1, 34125 Trieste, Italy
| | - Marina Rubini
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland;
| | - Mauro F. A. Adamo
- Department of Chemistry, Centre for Synthesis and Chemical Biology (CSCB), RCSI, 123 St. Stephens Green, Dublin 2, Ireland;
| | - Marco Scocchi
- Department of Life Sciences, University of Trieste, Via L. Giorgieri, 5, Q Building, 34127 Trieste, Italy; (M.S.); (A.T.); (R.G.)
| | - Michele Saviano
- Institute of Crystallography (IC), National Research Council (CNR), Via Amendola, 122, 70126 Bari, Italy;
| | - Alessandro Tossi
- Department of Life Sciences, University of Trieste, Via L. Giorgieri, 5, Q Building, 34127 Trieste, Italy; (M.S.); (A.T.); (R.G.)
| | - Renato Gennaro
- Department of Life Sciences, University of Trieste, Via L. Giorgieri, 5, Q Building, 34127 Trieste, Italy; (M.S.); (A.T.); (R.G.)
| | - Andrea Caporale
- Institute of Crystallography (IC), National Research Council (CNR), c/o Area Science Park, S.S. 14 Km 163.5, Basovizza, 34149 Trieste, Italy
| |
Collapse
|
36
|
Zhang Y, Chen M, Zhou S, Han H, Zhang M, Qiu H. A carbonylative coupling approach to alkyl stationary phases with variable embedded carbamate groups for high-performance liquid chromatography. J Chromatogr A 2021; 1661:462718. [PMID: 34875517 DOI: 10.1016/j.chroma.2021.462718] [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: 07/13/2021] [Revised: 11/12/2021] [Accepted: 11/26/2021] [Indexed: 12/15/2022]
Abstract
A highly efficient carbonylative coupling method for the preparation of alkyl stationary phases with variable numbers of carbamate groups was established. The effectiveness of such method was verified through elemental analysis, X-ray photoelectron spectroscopy and solid-state 13C nuclear magnetic resonance spectroscopy of three as-synthesized stationary phases bearing different alkyl chains and different numbers of carbamate groups (octadecyl/one carbamate group, C18C; docosyl/three carbamate groups, C22C3; triacontyl/two carbamate groups, C30C2). The comparative evaluation of these stationary phases using a great variety of analytes, including three sets of isomers of alkylbenzenes, two sets of standard mixtures of polycyclic aromatic hydrocarbons (SRM 1647e and 869b), nine polychlorinated biphenyls, fiveteen N-substituted ureas, ten sulfonylureas, five xanthines and some other phytonutrients, revealed their remarkable applicability in reversed-phase liquid chromatography. Notably, the intercalated carbamate groups rendered the resultant stationary phases compatible with 100% aqueous mobile phase. The suppression of silanol activity was positively related to the number of polar groups embedded in the bonded selector, and the smallest peak tailing factor (1.14) for amitriptyline was obtained by C22C3. The molecular shape-related selectivity was found to be more closely related to the length of the selector's aliphatic chain, as supported by the lowest αTBN/BaP value (0.31) by C30C2. These carbamate-embedded alkyl stationary phases constituted another class of polar-embedded stationary phases possessing a single type of functional ligand.
Collapse
Affiliation(s)
- Yujie Zhang
- School of Chemistry and Chemical Engineering, Huaiyin Normal University, Huai'an, 223000, China; CAS Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Min Chen
- Jiangsu Hanbon Science & Technology Co., Ltd., Huai'an, 223000, China
| | - Shouyong Zhou
- School of Chemistry and Chemical Engineering, Huaiyin Normal University, Huai'an, 223000, China
| | - Haifeng Han
- Jiangsu Hanbon Science & Technology Co., Ltd., Huai'an, 223000, China; CAS Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Mingliang Zhang
- Jiangsu Hanbon Science & Technology Co., Ltd., Huai'an, 223000, China; CAS Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou, 730000, China.
| | - Hongdeng Qiu
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou, 730000, China; College of Chemistry, Zhengzhou University, Zhengzhou, 450001, China.
| |
Collapse
|
37
|
Morioka K, Wakamatsu K, Tsurumaki E, Toyota S. Synthesis, Structures, and Properties of Helically Fused Anthraquinones with Unusually Close Carbonyl-Carbonyl Contacts. Chemistry 2021; 28:e202103694. [PMID: 34762325 DOI: 10.1002/chem.202103694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Indexed: 11/08/2022]
Abstract
Electron-deficient aromatic ketones consisting of three fused anthraquinone units were synthesized by oxidation of the corresponding fused anthracenes. X-ray analysis revealed that these compounds had nonplanar helical structures with unusual contacts, C=O⋅⋅⋅C=O 2.467 Å, between the inner carbonyl groups. The role of n⋅⋅⋅π* interactions in the short contacts was evaluated using a noncovalent interaction plot and natural bond orbital analysis. The dynamic process involving helical inversion was observed by the variable temperature 1 H NMR measurement of a derivative with 2,4,6-trimethylphenyl groups, and the barrier was estimated to be 77 kJ mol-1 . DFT calculations indicated that the helical inversion proceeded via a multistep mechanism. The characteristic spectroscopic and electrochemical data due to the electron-deficient anthraquinone units and the sterically congested carbonyl groups are discussed with the aid of DFT calculations.
Collapse
Affiliation(s)
- Kozue Morioka
- Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8551, Japan
| | - Kan Wakamatsu
- Department of Chemistry, Faculty of Science, Okayama University of Science, 1-1 Ridaicho, Kita-ku, Okayama, 700-0005, Japan
| | - Eiji Tsurumaki
- Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8551, Japan
| | - Shinji Toyota
- Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8551, Japan
| |
Collapse
|
38
|
Vik EC, Li P, Madukwe DO, Karki I, Tibbetts GS, Shimizu KD. Analysis of the Orbital and Electrostatic Contributions to the Lone Pair-Aromatic Interaction Using Molecular Rotors. Org Lett 2021; 23:8179-8182. [PMID: 34670094 DOI: 10.1021/acs.orglett.1c02878] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The attractive interaction between carbonyl oxygens and the π-face of aromatic surfaces was studied using N-phenylimide molecular rotors. The C═O···Ar interactions could stabilize the transition states but were half the strength of comparable C═O···C═O interactions. The C═O···Ar interaction had a significant electrostatic component but only a small orbital delocalization component.
Collapse
Affiliation(s)
- Erik C Vik
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Ping Li
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Daniel O Madukwe
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Ishwor Karki
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Gabriel S Tibbetts
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Ken D Shimizu
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| |
Collapse
|
39
|
Broadband dielectric relaxation spectroscopy and molecular dynamics simulation study of paracetamol-propylene glycol solutions. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
40
|
Wang W, Li X, Zhou PP, Wang Y. Catalysis with Supramolecular Carbon-Bonding Interactions. Angew Chem Int Ed Engl 2021; 60:22717-22721. [PMID: 34352156 DOI: 10.1002/anie.202108973] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/02/2021] [Indexed: 12/14/2022]
Abstract
Herein, we describe a new catalysis platform, supramolecular carbon-bonding catalysis, which exploits the highly directional weak interactions between carbon centers of catalysts and electron donors to drive chemical reactions. To demonstrate this catalysis approach, we discovered a class of cyclopropane derivatives incorporated with carbonyl, ester and cyano groups as catalysts which showed general catalysis capability in different types of benchmark reactions. Among these typical examples, a challenging tail-to-head terpene cyclization can be achieved by supramolecular carbon-bonding catalysis. The co-crystal structures of catalyst and electron donors, comparison experiments, and titrations support a catalysis mode of carbon-bonding activation of Lewis basic reactants.
Collapse
Affiliation(s)
- Wei Wang
- School of Chemistry and Chemical Engineering, Key Laboratory of the Colloid and Interface Chemistry, Ministry of Education, Shandong University, Jinan, 250100, China
| | - Xinxin Li
- School of Chemistry and Chemical Engineering, Key Laboratory of the Colloid and Interface Chemistry, Ministry of Education, Shandong University, Jinan, 250100, China
| | - Pan-Pan Zhou
- Key Laboratory of Advanced Catalysis of Gansu Province, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, China
| | - Yao Wang
- School of Chemistry and Chemical Engineering, Key Laboratory of the Colloid and Interface Chemistry, Ministry of Education, Shandong University, Jinan, 250100, China.,State Key Laboratory of Crystal Materials, Shandong University, Jinan, 250100, China
| |
Collapse
|
41
|
Wang W, Li X, Zhou P, Wang Y. Catalysis with Supramolecular Carbon‐Bonding Interactions. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202108973] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Wei Wang
- School of Chemistry and Chemical Engineering Key Laboratory of the Colloid and Interface Chemistry Ministry of Education, Shandong University Jinan 250100 China
| | - Xinxin Li
- School of Chemistry and Chemical Engineering Key Laboratory of the Colloid and Interface Chemistry Ministry of Education, Shandong University Jinan 250100 China
| | - Pan‐Pan Zhou
- Key Laboratory of Advanced Catalysis of Gansu Province College of Chemistry and Chemical Engineering Lanzhou University Lanzhou 730000 China
| | - Yao Wang
- School of Chemistry and Chemical Engineering Key Laboratory of the Colloid and Interface Chemistry Ministry of Education, Shandong University Jinan 250100 China
- State Key Laboratory of Crystal Materials Shandong University Jinan 250100 China
| |
Collapse
|
42
|
Abstract
In this work, a computational study on the ionization potentials (IPs) of the formaldehyde trimer, (H2CO)3, is presented. Twelve lowest-lying vertical IPs were determined through the use of the coupled-cluster level of theory using correlation consistent basis sets with extrapolation to the complete basis set limit and consideration of core electron correlation effects. Specifically, the equation-of-motion ionization potential coupled-cluster with single and double excitations method with the aug-cc-pVnZ and aug-cc-pCVnZ (n = D and T) basis sets was used. The Feller-Peterson-Dixon (FPD) composite approach was employed to provide accurate IPs, and eight conformations of (H2CO)3 were considered. The FPD IPs determined for (H2CO)3 were found to be systematically lower than those computed for the dimer and monomer of H2CO in the pattern IP(monomer) > IP(dimer) > IP(trimer) for a given IP. In addition, the IPs calculated when considering only the more stable conformation (C0) are in good agreement with those obtained using the eight conformations of the H2CO trimer, and thus, the actual conformation played only a minor role in determining such properties in the present case. By providing first accurate IP results for the H2CO trimer, we hope to motivate future experimental and computational investigations (e.g., studies involving photoionization) that rely on such quantities.
Collapse
Affiliation(s)
- Gabriel L C de Souza
- Departamento de Química, Universidade Federal de Mato Grosso, Cuiabá, Mato Grosso 78060-900, Brazil
| | - Kirk A Peterson
- Department of Chemistry, Washington State University, Pullman, Washington 99164, USA
| |
Collapse
|
43
|
Henderson WR, Liu G, Abboud KA, Castellano RK. Tuning Supramolecular Polymer Assembly through Stereoelectronic Interactions. J Am Chem Soc 2021; 143:12688-12698. [PMID: 34346675 DOI: 10.1021/jacs.1c05522] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The supramolecular polymerization of 2,11-dithia[3.3]paracyclophanes through self-complementary intermolecular and transannular amide hydrogen bonding is presented. An n → π* interaction between the amide hydrogen bonding units and the central bridging atom results from the single-point exchange of a carbon atom for a sulfur atom. This orbital donor-acceptor interaction can be strengthened by oxidizing the sulfide to a sulfone which acts to shorten the donor···acceptor distance and increase orbital overlap. Experimental signatures of the increased n → π* interaction include larger isodesmic polymerization elongation constants in solution, changes in characteristic bond stretching frequencies, and geometric/structural changes evaluated by X-ray crystallography. The experimental data are supported by extensive computational investigations of both assembling and nonassembling 2,11-dithia[3.3]paracyclophanes as well as a rationally designed model system to confirm the role of stereoelectronic effects on supramolecular polymer assembly.
Collapse
Affiliation(s)
- Will R Henderson
- George & Josephine Butler Polymer Research Laboratory, Center for Macromolecular Science & Engineering, Department of Chemistry, University of Florida, P.O. Box 117200 Gainesville, Florida 32611-7200, United States
| | - Guancen Liu
- George & Josephine Butler Polymer Research Laboratory, Center for Macromolecular Science & Engineering, Department of Chemistry, University of Florida, P.O. Box 117200 Gainesville, Florida 32611-7200, United States
| | - Khalil A Abboud
- George & Josephine Butler Polymer Research Laboratory, Center for Macromolecular Science & Engineering, Department of Chemistry, University of Florida, P.O. Box 117200 Gainesville, Florida 32611-7200, United States
| | - Ronald K Castellano
- George & Josephine Butler Polymer Research Laboratory, Center for Macromolecular Science & Engineering, Department of Chemistry, University of Florida, P.O. Box 117200 Gainesville, Florida 32611-7200, United States
| |
Collapse
|
44
|
Tamez-Fernández JF, Soto-Suárez FM, Estrada-Chavarría YD, Quijano-Quiñones RF, Toscano RA, Cuétara-Guadarrama F, Duarte-Alaniz V, Ibarra-Rivera TR, Quiroz-García B, Martínez-Otero D, Ramírez-Gualito K, Barquera-Lozada JE, Rivas-Galindo VM, Cuevas G. Effect of the n O → π* C═O Interaction on the Conformational Preference of 1,3-Diketones: A Case Study of Riolozatrione Derivatives. J Org Chem 2021; 86:9540-9551. [PMID: 34210132 DOI: 10.1021/acs.joc.1c00847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The cyclopropane ring-opening reaction of riolozatrione, a natural product obtained from Jatropha dioica, afforded a 2,2-disubstituted 1,3-cyclohexandione displaying an alkyl methyl ether group at position 5. The conformational analysis of this product showed a high preference for the trans-diaxial conformation in both solution and solid state. Such conformation was possible from the noncovalent intramolecular nX → π*C═O interactions (X = an element having an unshared electron pair), allowing the determination of the interaction energies. Since the nX → π*C═O interactions can be regarded as additive, the energy values ranged from 4.52 to 6.51 kcal mol-1 for each carbonyl group with a strong dependency on the interatomic distances. The rigorous analysis of the electron density in the topological theory of atoms in molecules framework clearly shows that the origin of O-C═O interactions are through the nO → π*C═O electron transfer mechanism. Such interactions are slightly weaker than a canonical hydrogen bond but seemingly stronger than a van der Waals interaction. This interaction must be considered as a stereoelectronic effect due the electronic transfer between the interacting groups, which are limited by their relative stereochemistry and can be represented by a bond-no bond interaction, causing the pyramidalization of the carbonyl, which is the charge acceptor group.
Collapse
Affiliation(s)
- Juan F Tamez-Fernández
- Facultad de Medicina, Departamento de Química Analítica, Universidad Autonoma de Nuevo Leon, 66455 Monterrey, Nuevo León, Mexico
| | - Fátima M Soto-Suárez
- Instituto de Química, Circuito Exterior, Ciudad Universitaria, Universidad Nacional Autónoma de México, Delegación Coyoacán, 04510 Ciudad de México, Mexico
| | - Yolanda D Estrada-Chavarría
- Facultad de Medicina, Departamento de Química Analítica, Universidad Autonoma de Nuevo Leon, 66455 Monterrey, Nuevo León, Mexico
| | - Ramiro F Quijano-Quiñones
- Facultad de Química, Universidad Autónoma de Yucatán. Laboratorio de Química Teórica, Calle 43 No. 613 por calle 90, 97069 Colonia Inalámbrica, Mérida Yucatán, Mexico
| | - Rubén A Toscano
- Instituto de Química, Circuito Exterior, Ciudad Universitaria, Universidad Nacional Autónoma de México, Delegación Coyoacán, 04510 Ciudad de México, Mexico
| | - Fabián Cuétara-Guadarrama
- Instituto de Química, Circuito Exterior, Ciudad Universitaria, Universidad Nacional Autónoma de México, Delegación Coyoacán, 04510 Ciudad de México, Mexico
| | - Víctor Duarte-Alaniz
- Instituto de Química, Circuito Exterior, Ciudad Universitaria, Universidad Nacional Autónoma de México, Delegación Coyoacán, 04510 Ciudad de México, Mexico
| | - Tannya R Ibarra-Rivera
- Facultad de Medicina, Departamento de Química Analítica, Universidad Autonoma de Nuevo Leon, 66455 Monterrey, Nuevo León, Mexico
| | - Beatriz Quiroz-García
- Instituto de Química, Circuito Exterior, Ciudad Universitaria, Universidad Nacional Autónoma de México, Delegación Coyoacán, 04510 Ciudad de México, Mexico
| | - Diego Martínez-Otero
- Carretera Toluca-Atlacomulco, Centro Conjunto de Investigación en Química Sustentable UAEM-UNAM, km 14.5, Toluca, 50200 Estado de México, Mexico
| | - Karla Ramírez-Gualito
- Facultad de Ingeniería, Universidad Anáhuac México, Avenida Universidad Anáhuac 46, Col. Lomas Anáhuac, Huixquilucan, 52786 Estado de México, Mexico
| | - José Enrique Barquera-Lozada
- Instituto de Química, Circuito Exterior, Ciudad Universitaria, Universidad Nacional Autónoma de México, Delegación Coyoacán, 04510 Ciudad de México, Mexico
| | - Verónica M Rivas-Galindo
- Facultad de Medicina, Departamento de Química Analítica, Universidad Autonoma de Nuevo Leon, 66455 Monterrey, Nuevo León, Mexico
| | - Gabriel Cuevas
- Instituto de Química, Circuito Exterior, Ciudad Universitaria, Universidad Nacional Autónoma de México, Delegación Coyoacán, 04510 Ciudad de México, Mexico
| |
Collapse
|
45
|
Pollastrini M, Lipparini F, Pasquinelli L, Balzano F, Barretta GU, Pescitelli G, Angelici G. A Proline Mimetic for the Design of New Stable Secondary Structures: Solvent-Dependent Amide Bond Isomerization of ( S)-Indoline-2-carboxylic Acid Derivatives. J Org Chem 2021; 86:7946-7954. [PMID: 34080867 PMCID: PMC8456495 DOI: 10.1021/acs.joc.1c00184] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Indexed: 12/22/2022]
Abstract
A thorough experimental and computational study on the conformational properties of (S)-indoline-2-carboxylic acid derivatives has been conducted. Methyl (S)-1-acetylindoline-2-carboxylate, both a mimetic of proline and phenylalanine, shows a remarkable tendency toward the cis amide isomer when dissolved in polar solvents. This behavior is opposite to the general preference of proline for the trans isomer, making indoline-2-carboxylic acid a good candidate for the design of different secondary structures and new materials.
Collapse
Affiliation(s)
- Matteo Pollastrini
- Dipartimento di Chimica e Chimica Industriale,
Università di Pisa, Via G. Moruzzi 13, 56124 Pisa,
Italy
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale,
Università di Pisa, Via G. Moruzzi 13, 56124 Pisa,
Italy
| | - Luca Pasquinelli
- Dipartimento di Chimica e Chimica Industriale,
Università di Pisa, Via G. Moruzzi 13, 56124 Pisa,
Italy
| | - Federica Balzano
- Dipartimento di Chimica e Chimica Industriale,
Università di Pisa, Via G. Moruzzi 13, 56124 Pisa,
Italy
| | - Gloria Uccello Barretta
- Dipartimento di Chimica e Chimica Industriale,
Università di Pisa, Via G. Moruzzi 13, 56124 Pisa,
Italy
| | - Gennaro Pescitelli
- Dipartimento di Chimica e Chimica Industriale,
Università di Pisa, Via G. Moruzzi 13, 56124 Pisa,
Italy
| | - Gaetano Angelici
- Dipartimento di Chimica e Chimica Industriale,
Università di Pisa, Via G. Moruzzi 13, 56124 Pisa,
Italy
| |
Collapse
|
46
|
Sahariah B, Sarma BK. Spectroscopic evidence of n → π* interactions involving carbonyl groups. Phys Chem Chem Phys 2021; 22:26669-26681. [PMID: 33226050 DOI: 10.1039/d0cp03557b] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
n → π* has emerged as an important noncovalent interaction that can affect the conformations of both small- and macromolecules including peptides and proteins. Carbonyl-carbonyl (COCO) n → π* interactions involving CO groups are well studied. Recent studies have shown that the COCO n → π* interactions are the most abundant secondary interactions in proteins with a frequency of 33 interactions per 100 residues and, among the various secondary interactions, n → π* interactions are expected to provide the highest enthalpic contributions to the conformational stability of globular proteins. However, n → π* interactions are relatively weak and provide an average stabilization of about 0.25 kcal mol-1 per interaction in proteins. The strongest n → π* interaction could be as strong as a moderate hydrogen bond. Therefore, it is challenging to detect and quantify these weak interactions, especially in solution in the presence of perturbation from other intermolecular interactions. Accordingly, spectroscopic investigations that can provide direct evidence of n → π* interaction are limited, and the majority of papers published in this area have relied on X-ray crystallography and/or theoretical calculations to establish the presence of this interaction. The aim of this perspective is to discuss the studies where a spectroscopic signature in support of n → π* interaction was observed. As the "n → π* interaction" is a relatively new terminology, there remains the possibility of there being earlier studies where spectroscopic evidence for n → π* interactions was obtained but it was not discussed in light of the n → π* terminology. We noticed several such studies and, as can be expected, these studies were often overlooked in the discussion of n → π* interactions in the recent literature. In this perspective, we have also discussed these studies and provided computational support for the presence of n → π* interaction.
Collapse
Affiliation(s)
- Biswajit Sahariah
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore 560064, India.
| | | |
Collapse
|
47
|
Suryaprasad B, Chandra S, Ramanathan N, Sundararajan K. Pentavalent P…π phosphorus bonding with associated Cl…π halogen bonding in influencing the geometry of POCl3-Phenylacetylene heterodimers: Evidence from matrix isolation infrared spectroscopy and ab initio computations. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129288] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
48
|
Daicho K, Ozawa Y, Sugimoto K, Abe M. A pyrazine‐bridged trimer of oxo‐centered triruthenium–carbonyl clusters and the supramolecular assembly built from multiple noncovalent contacts. J CHIN CHEM SOC-TAIP 2020. [DOI: 10.1002/jccs.202000491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Keita Daicho
- Graduate School of Material Science University of Hyogo Ako‐gun Japan
| | - Yoshiki Ozawa
- Graduate School of Material Science University of Hyogo Ako‐gun Japan
| | - Kunihisa Sugimoto
- Diffraction & Scattering Division, Japan Synchrotron Radiation Research Institute (JASRI) Sayo‐gun Japan
| | - Masaaki Abe
- Graduate School of Material Science University of Hyogo Ako‐gun Japan
| |
Collapse
|
49
|
Abstract
The fundamental underpinnings of noncovalent bonds are presented, focusing on the σ-hole interactions that are closely related to the H-bond. Different means of assessing their strength and the factors that control it are discussed. The establishment of a noncovalent bond is monitored as the two subunits are brought together, allowing the electrostatic, charge redistribution, and other effects to slowly take hold. Methods are discussed that permit prediction as to which site an approaching nucleophile will be drawn, and the maximum number of bonds around a central atom in its normal or hypervalent states is assessed. The manner in which a pair of anions can be held together despite an overall Coulombic repulsion is explained. The possibility that first-row atoms can participate in such bonds is discussed, along with the introduction of a tetrel analog of the dihydrogen bond.
Collapse
Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, USA
| |
Collapse
|
50
|
Chandra S, Suryaprasad B, Ramanathan N, Sundararajan K. Dominance of unique Pπ phosphorus bonding with π donors: evidence using matrix isolation infrared spectroscopy and computational methodology. Phys Chem Chem Phys 2020; 22:20771-20791. [PMID: 32909555 DOI: 10.1039/d0cp02880k] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Albeit the first account of hypervalentπ interactions has been reported with halogenπ interactions, the feasibility of their extension to other hypervalent atoms as possible Lewis acids is still open. In this work, the role of phosphorus as an acceptor from the π electron cloud (Pπ pnicogen or phosphorus bonding) in PCl3-C2H2 and PCl3-C2H4 heterodimers is explored, by combining matrix isolation infrared spectroscopy with ab initio and DFT computational methodologies. The respective potential energy surfaces of the PCl3-C2H2 and PCl3-C2H4 heterodimers reveal unique minima stabilized by a concert of reasonably strong to weak interactions, of which Pπ phosphorus bonding was energetically dominant. Heterodimers, trimers and tetramers bound primarily by this unique phosphorus bond were generated at low temperatures. The dominance of phosphorus bonding in the PCl3-C2H2 and PCl3-C2H4 heterodimers over other interactions (such as Hπ, HCl, HP, Clπ and lone pair-π interactions) was confirmed and substantiated using extended quantum theory of atoms in molecules, natural bond orbital, electrostatic potential mapping and energy decomposition analyses. The following inferences in correlation with results from non-covalent-interaction analysis offer a complete understanding of the nature of the Pπ phosphorus bonding interactions. The significance of electrostatic forces kinetically favoring the formation of phosphorus bonded heterodimers, in addition to thermodynamic stabilization, is demonstrated experimentally.
Collapse
Affiliation(s)
- Swaroop Chandra
- Homi Bhabha National Institute, Materials Chemistry & Metal Fuel Cycle Group, Indira Gandhi Center for Atomic Research, Kalpakkam - 603102, Tamil Nadu, India.
| | - B Suryaprasad
- Homi Bhabha National Institute, Materials Chemistry & Metal Fuel Cycle Group, Indira Gandhi Center for Atomic Research, Kalpakkam - 603102, Tamil Nadu, India.
| | - N Ramanathan
- Homi Bhabha National Institute, Materials Chemistry & Metal Fuel Cycle Group, Indira Gandhi Center for Atomic Research, Kalpakkam - 603102, Tamil Nadu, India.
| | - K Sundararajan
- Homi Bhabha National Institute, Materials Chemistry & Metal Fuel Cycle Group, Indira Gandhi Center for Atomic Research, Kalpakkam - 603102, Tamil Nadu, India.
| |
Collapse
|