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Mali SN, Pandey A. Multiple QSAR and molecular modelling for identification of potent human adenovirus inhibitors. J INDIAN CHEM SOC 2021. [DOI: 10.1016/j.jics.2021.100082] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Breijyeh Z, Karaman R. Enzyme Models-From Catalysis to Prodrugs. Molecules 2021; 26:molecules26113248. [PMID: 34071328 PMCID: PMC8198240 DOI: 10.3390/molecules26113248] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/22/2021] [Accepted: 05/26/2021] [Indexed: 11/24/2022] Open
Abstract
Enzymes are highly specific biological catalysts that accelerate the rate of chemical reactions within the cell. Our knowledge of how enzymes work remains incomplete. Computational methodologies such as molecular mechanics (MM) and quantum mechanical (QM) methods play an important role in elucidating the detailed mechanisms of enzymatic reactions where experimental research measurements are not possible. Theories invoked by a variety of scientists indicate that enzymes work as structural scaffolds that serve to bring together and orient the reactants so that the reaction can proceed with minimum energy. Enzyme models can be utilized for mimicking enzyme catalysis and the development of novel prodrugs. Prodrugs are used to enhance the pharmacokinetics of drugs; classical prodrug approaches focus on alternating the physicochemical properties, while chemical modern approaches are based on the knowledge gained from the chemistry of enzyme models and correlations between experimental and calculated rate values of intramolecular processes (enzyme models). A large number of prodrugs have been designed and developed to improve the effectiveness and pharmacokinetics of commonly used drugs, such as anti-Parkinson (dopamine), antiviral (acyclovir), antimalarial (atovaquone), anticancer (azanucleosides), antifibrinolytic (tranexamic acid), antihyperlipidemia (statins), vasoconstrictors (phenylephrine), antihypertension (atenolol), antibacterial agents (amoxicillin, cephalexin, and cefuroxime axetil), paracetamol, and guaifenesin. This article describes the works done on enzyme models and the computational methods used to understand enzyme catalysis and to help in the development of efficient prodrugs.
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Dual demeanour of norcantharidin derived dicarboxamides in acidic media: An insight. Tetrahedron 2019. [DOI: 10.1016/j.tet.2019.07.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Design, synthesis, and in vitro kinetics study of atenolol prodrugs for the use in aqueous formulations. ScientificWorldJournal 2014; 2014:248651. [PMID: 24526887 PMCID: PMC3913492 DOI: 10.1155/2014/248651] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 12/01/2013] [Indexed: 02/07/2023] Open
Abstract
Based on DFT, MP2, and the density functional from Truhlar group (hybrid GGA: MPW1k) calculations for an acid-catalyzed hydrolysis of nine Kirby's N-alkylmaleamic acids and two atenolol prodrugs were designed. The calculations demonstrated that the amide bond cleavage is due to intramolecular nucleophilic catalysis by the adjacent carboxylic acid group and the rate-limiting step is determined based on the nature of the amine leaving group. In addition, a linear correlation of the calculated and experimental rate values has drawn credible basis for designing atenolol prodrugs that are bitterless, are stable in neutral aqueous solutions, and have the potential to release the parent drug in a sustained release manner. For example, based on the calculated B3LYP/6-31 G (d,p) rates, the predicted t1/2 (a time needed for 50% of the prodrug to be converted into drug) values for atenolol prodrugs ProD 1-ProD 2 at pH 2 were 65.3 hours (6.3 hours as calculated by GGA: MPW1K) and 11.8 minutes, respectively. In vitro kinetic study of atenolol prodrug ProD 1 demonstrated that the t1/2 was largely affected by the pH of the medium. The determined t1/2 values in 1N HCl, buffer pH 2, and buffer pH 5 were 2.53, 3.82, and 133 hours, respectively.
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Karaman R. Prodrugs Design Based on Inter- and Intramolecular Chemical Processes. Chem Biol Drug Des 2013; 82:643-68. [DOI: 10.1111/cbdd.12224] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 08/13/2013] [Accepted: 08/16/2013] [Indexed: 01/29/2023]
Affiliation(s)
- Rafik Karaman
- Bioorganic Chemistry Department; Faculty of Pharmacy; Al-Quds University; P.O. Box 20002 Jerusalem Palestine
- Department of Science; University of Basilicata; Via dell'Ateneo Lucano 10 85100 Potenza Italy
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Design, synthesis and in vitro kinetic study of tranexamic acid prodrugs for the treatment of bleeding conditions. J Comput Aided Mol Des 2013; 27:615-35. [PMID: 23881217 DOI: 10.1007/s10822-013-9666-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 07/06/2013] [Indexed: 02/07/2023]
Abstract
Based on density functional theory (DFT) calculations for the acid-catalyzed hydrolysis of several maleamic acid amide derivatives four tranexamic acid prodrugs were designed. The DFT results on the acid catalyzed hydrolysis revealed that the reaction rate-limiting step is determined on the nature of the amine leaving group. When the amine leaving group was a primary amine or tranexamic acid moiety, the tetrahedral intermediate collapse was the rate-limiting step, whereas in the cases by which the amine leaving group was aciclovir or cefuroxime the rate-limiting step was the tetrahedral intermediate formation. The linear correlation between the calculated DFT and experimental rates for N-methylmaleamic acids 1-7 provided a credible basis for designing tranexamic acid prodrugs that have the potential to release the parent drug in a sustained release fashion. For example, based on the calculated B3LYP/6-31G(d,p) rates the predicted t1/2 (a time needed for 50 % of the prodrug to be converted into drug) values for tranexamic acid prodrugs ProD 1-ProD 4 at pH 2 were 556 h [50.5 h as calculated by B3LYP/311+G(d,p)] and 6.2 h as calculated by GGA: MPW1K), 253 h, 70 s and 1.7 h, respectively. Kinetic study on the interconversion of the newly synthesized tranexamic acid prodrug ProD 1 revealed that the t1/2 for its conversion to the parent drug was largely affected by the pH of the medium. The experimental t1/2 values in 1 N HCl, buffer pH 2 and buffer pH 5 were 54 min, 23.9 and 270 h, respectively.
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Karaman R, Amly W, Scrano L, Mecca G, Bufo SA. Computationally designed prodrugs of statins based on Kirby's enzyme model. J Mol Model 2013; 19:3969-82. [PMID: 23835602 DOI: 10.1007/s00894-013-1929-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 06/17/2013] [Indexed: 12/14/2022]
Abstract
DFT calculations at B3LYP/6-31G(d,p) for intramolecular proton transfer in Kirby's enzyme models 1-7 demonstrated that the reaction rate is dependent on the distance between the two reacting centers, rGM, and the hydrogen bonding angle, α, and the rate of the reaction is linearly correlated with rGM and α. Based on these calculation results three simvastatin prodrugs were designed with the potential to provide simvastatin with higher bioavailability. For example, based on the calculated log EM for the three proposed prodrugs, the interconversion of simvastatin prodrug ProD 3 to simvastatin is predicted to be about 10 times faster than that of either simvastatin prodrug ProD 1 or simvastatin ProD 2. Hence, the rate by which the prodrug releases the statin drug can be determined according to the structural features of the promoiety (Kirby's enzyme model).
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Affiliation(s)
- Rafik Karaman
- Bioorganic Chemistry Department, Faculty of Pharmacy, Al-Quds University, P. O. Box 20002, Jerusalem, Palestine.
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Karaman R, Fattash B, Qtait A. The future of prodrugs – design by quantum mechanics methods. Expert Opin Drug Deliv 2013; 10:713-29. [DOI: 10.1517/17425247.2013.786699] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Karaman R, Karaman D, Zeiadeh I. Computationally-designed phenylephrine prodrugs – a model for enhancing bioavailability. Mol Phys 2013. [DOI: 10.1080/00268976.2013.779395] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Prathyusha V, Priyakumar UD. Role of conformational properties on the transannular Diels–Alder reactivity of macrocyclic trienes with varying linker lengths. RSC Adv 2013. [DOI: 10.1039/c3ra42045k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Prodrugs of fumarate esters for the treatment of psoriasis and multiple sclerosis—a computational approach. J Mol Model 2012; 19:439-52. [DOI: 10.1007/s00894-012-1554-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2012] [Accepted: 07/30/2012] [Indexed: 10/27/2022]
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Dahan A, Khamis M, Agbaria R, Karaman R. Targeted prodrugs in oral drug delivery: the modern molecular biopharmaceutical approach. Expert Opin Drug Deliv 2012; 9:1001-13. [PMID: 22703376 DOI: 10.1517/17425247.2012.697055] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
INTRODUCTION The molecular revolution greatly impacted the field of drug design and delivery in general, and the utilization of the prodrug approach in particular. The increasing understanding of membrane transporters has promoted a novel 'targeted-prodrug' approach utilizing carrier-mediated transport to increase intestinal permeability, as well as specific enzymes to promote activation to the parent drug. AREAS COVERED This article provides the reader with a concise overview of this modern approach to prodrug design. Targeting the oligopeptide transporter PEPT1 for absorption and the serine hydrolase valacyclovirase for activation will be presented as examples for the successful utilization of this approach. Additionally, the use of computational approaches, such as DFT and ab initio molecular orbital methods, in modern prodrugs design will be discussed. EXPERT OPINION Overall, in the coming years, more and more information will undoubtedly become available regarding intestinal transporters and potential enzymes that may be exploited for the targeted modern prodrug approach. Hence, the concept of prodrug design can no longer be viewed as merely a chemical modification to solve problems associated with parent compounds. Rather, it opens promising opportunities for precise and efficient drug delivery, as well as enhancement of treatment options and therapeutic efficacy.
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Affiliation(s)
- Arik Dahan
- Ben-Gurion University of the Negev, School of Pharmacy, Faculty of Health Sciences, Department of Clinical Pharmacology, P.O. Box 653, Beer-Sheva 84105, Israel.
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Prathyusha V, Ramakrishna S, Priyakumar UD. Transannular Diels–Alder Reactivities of 14-Membered Macrocylic Trienes and Their Relationship with the Conformational Preferences of the Reactants: A Combined Quantum Chemical and Molecular Dynamics Study. J Org Chem 2012; 77:5371-80. [DOI: 10.1021/jo300812q] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- V. Prathyusha
- Center for Computational
Natural Sciences and Bioinformatics, International Institute of Information Technology,
Hyderabad 500 032, India
| | - S. Ramakrishna
- Center for Computational
Natural Sciences and Bioinformatics, International Institute of Information Technology,
Hyderabad 500 032, India
| | - U. Deva Priyakumar
- Center for Computational
Natural Sciences and Bioinformatics, International Institute of Information Technology,
Hyderabad 500 032, India
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Karaman R, Dajani KK, Qtait A, Khamis M. Prodrugs of acyclovir--a computational approach. Chem Biol Drug Des 2012; 79:819-34. [PMID: 22260647 DOI: 10.1111/j.1747-0285.2012.01335.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Density functional theory calculation results demonstrated that the efficiency of the acid-catalyzed hydrolysis of Kirby's acid amides 1-15 is strongly dependent on the substitution on the C-C double bond and the nature of the amide N-alkyl group. Further, the results established that while in the gas phase the hydrolysis rate-limiting step is the tetrahedral intermediate formation in polar solvents such as water, the rate-limiting step could be either the formation or the collapse of the tetrahedral intermediate depending on the substitution on the C-C double bond and on the amide nitrogen substituent. Based on a linear correlation between the calculated and experimental effective molarities, the study on the systems reported herein could provide a good basis for designing prodrug systems that are less hydrophilic than their parental drugs and can be used, in different dosage forms, to release the parent drug in a controlled manner. For example, based on the calculated log effective molarities values, the predicted t(1/2) (a time needed for 50% of the reactant to be hydrolyzed to products) for acyclovir prodrugs, ProD 1-4, was 29.2 h, 6097 days, 4.6 min, and 8.34 h, respectively. Hence, the rate by which acyclovir prodrug releases acyclovir can be determined according to the structural features of the linker (Kirby's acid amide moiety).
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Affiliation(s)
- Rafik Karaman
- Faculty of Pharmacy, Al-Quds University, Jerusalem, Palestine.
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Stojanović M, Marković R, Kleinpeter E, Baranac-Stojanović M. Synthesis of thiazolidine-fused heterocycles via exo-mode cyclizations of vinylogous N-acyliminium ions. Org Biomol Chem 2012; 10:575-89. [DOI: 10.1039/c1ob06451g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Stojanović M, Marković R, Kleinpeter E, Baranac-Stojanović M. endo-Mode cyclizations of vinylogous N-acyliminium ions as a route to the synthesis of condensed thiazolidines. Tetrahedron 2011. [DOI: 10.1016/j.tet.2011.10.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Karaman R. Analyzing the efficiency in intramolecular amide hydrolysis of Kirby’s N-alkylmaleamic acids – A computational approach. COMPUT THEOR CHEM 2011. [DOI: 10.1016/j.comptc.2011.07.025] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Karaman R. Computational-aided design for dopamine prodrugs based on novel chemical approach. Chem Biol Drug Des 2011; 78:853-63. [PMID: 21824329 DOI: 10.1111/j.1747-0285.2011.01208.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The goal of this project was to design novel dopamine prodrugs for the treatment of Parkinson's disease that can improve the overall biopharmaceutical profile of the current medications to enhance effectiveness and to ease the use of the medications. Based on Menger's study and other's kinetic studies on the cleavage reactions of some Kemp's acid amides to the corresponding amines and anhydrides, DFT calculations were made to find a candidate to be used as an efficient dopamine prodrug. The proposed dopamine prodrugs have a carboxylic group as a hydrophilic moiety and a hydrocarbon skeleton as a lipophilic moiety, where the combination of both groups ensures a moderate hydrophilic lipophilc balance value. The potential prodrugs are expected to give better bioavailability than the parental drug owing to improved absorption. Furthermore, the proposed prodrugs are believed to be more effective than l-dopa because the latter undergoes decarboxylation in the periphery before reaching the blood-brain barrier. Additionally, the predicted prodrugs can be used in different dosage forms (I.V., S.C., tablets, and others) because of their potential solubility in organic and aqueous media. It is expected that the proposed prodrugs will undergo cleavage reactions to release the parental dopamine drug with half-life time (t(½) ) of 12-20 h.
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Affiliation(s)
- Rafik Karaman
- Faculty of Pharmacy, Al-Quds University, P.O. Box 20002, Jerusalem, Palestine.
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Karaman R, Dajani K, Hallak H. Computer-assisted design for atenolol prodrugs for the use in aqueous formulations. J Mol Model 2011; 18:1523-40. [PMID: 21785934 DOI: 10.1007/s00894-011-1180-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2011] [Accepted: 07/04/2011] [Indexed: 11/24/2022]
Abstract
Based on stability studies on the drugs atenolol and propranolol and some of their derivatives it is believed that increasing the lipophilicity of the drug will lead to an increase in the stability of its aqueous solutions and will provide a prodrug system with the potential for releasing atenolol in a controlled manner. Using DFT theoretical calculations we have calculated an intramolecular acid catalyzed hydrolysis in nine maleamic (4-amino-4-oxo-2butenoic) acids (Kirby's N-alkylmaleamic acids), 1-9. The DFT calculations confirmed that the acid-catalyzed hydrolysis mechanism in these systems involves: (1) a proton transfer from the hydroxyl of the carboxyl group to the adjacent amide carbonyl carbon, (2) an approach of the carboxylate anion toward the protonated amide carbonyl carbon to form a tetrahedral intermediate; and (3) a collapse of the tetrahedral intermediate into products. Furthermore, DFT calculations in different media revealed that the reaction rate-limiting step depends on the reaction medium. In aqueous medium the rate-limiting step is the collapse of the tetrahedral intermediate whereas in the gas phase the formation of the tetrahedral intermediate is the rate-limiting step. Furthermore, the calculations establish that the acid-catalyzed hydrolysis efficiency is largely sensitive to the pattern of substitution on the carbon-carbon double bond. Based on the experimental t(1/2) (the time needed for the conversion of 50% of the reactants to products) and EM (effective molarity) values for processes 1-9 we have calculated the t(1/2) values for the conversion of the two prodrugs to the parental drug, atenolol. The calculated t(1/2) values for ProD 1-2 are predicted to be 65.3 hours and 11.8 minutes, respectively. Thus, the rate by which atenolol prodrug undergoes cleavage to release atenolol can be determined according to the nature of the linker of the prodrug (Kirby's N-alkylmaleamic acids 1-9).
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Affiliation(s)
- Rafik Karaman
- Faculty of Pharmacy, Al-Quds University, Box 20002, Jerusalem, Palestine.
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Computer-assisted design for paracetamol masking bitter taste prodrugs. J Mol Model 2011; 18:103-14. [PMID: 21491187 DOI: 10.1007/s00894-011-1040-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2011] [Accepted: 03/14/2011] [Indexed: 10/18/2022]
Abstract
It is believed that the bitter taste of paracetamol, a pain killer drug, is due to its hydroxyl group. Hence, it is expected that blocking the hydroxy group with a suitable linker could inhibit the interaction of paracetamol with its bitter taste receptor/s and hence masking its bitterness. Using DFT theoretical calculations we calculated proton transfers in ten different Kirby's enzyme models, 1-10. The calculation results revealed that the reaction rate is linearly correlated with the distance between the two reactive centers (r(GM)) and the angle of the hydrogen bonding (α) formed along the reaction pathway. Based on these results three novel tasteless paracetamol prodrugs were designed and the thermodynamic and kinetic parameters for their proton transfers were calculated. Based on the experimental t(1/2) (the time needed for the conversion of 50% of the reactants to products) and EM (effective molarity) values for processes 1-10 we have calculated the t(1/2) values for the conversion of the three prodrugs to the parental drug, paracetamol. The calculated t(1/2) values for ProD 1-3 were found to be 21.3 hours, 4.7 hours and 8 minutes, respectively. Thus, the rate by which the paracetamol prodrug undergoes cleavage to release paracetamol can be determined according to the nature of the linker of the prodrug (Kirby's enzyme model 1-10). Further, blocking the phenolic hydroxyl group by a linker moiety is believed to hinder the paracetamol bitterness.
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Karaman R. Analyzing the efficiency of proton transfer to carbon in Kirby’s enzyme model—a computational approach. Tetrahedron Lett 2011. [DOI: 10.1016/j.tetlet.2010.12.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Karaman R. Prodrugs of aza nucleosides based on proton transfer reaction. J Comput Aided Mol Des 2010; 24:961-70. [PMID: 20941527 DOI: 10.1007/s10822-010-9389-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Accepted: 10/01/2010] [Indexed: 10/19/2022]
Abstract
DFT calculation results for intramolecular proton transfer reactions in Kirby's enzyme models 1-7 reveal that the reaction rate is quite responsive to geometric disposition, especially to distance between the two reactive centers, r (GM), and the angle of attack, α (the hydrogen bonding angle). Hence, the study on the systems reported herein could provide a good basis for designing aza nucleoside prodrug systems that are less hydrophilic than their parental drugs and can be used, in different dosage forms, to release the parent drug in a controlled manner. For example, based on the calculated log EM, the cleavage process for prodrug 1ProD is predicted to be about 10¹⁰ times faster than that for prodrug 7ProD and about 10⁴ times faster than prodrug 3ProD: rate( 1ProD ) > rate( 3ProD ) > rate( 7ProD ). Hence, the rate by which the prodrug releases the aza nucleoside drug can be determined according to the structural features of the linker (Kirby's enzyme model).
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Affiliation(s)
- Rafik Karaman
- Faculty of Pharmacy, Al-Quds University, Jerusalem, Palestine.
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Karaman R, Pascal R. A computational analysis of intramolecularity in proton transfer reactions. Org Biomol Chem 2010; 8:5174-8. [PMID: 20848031 DOI: 10.1039/c0ob00252f] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hydrogen bonds along which most proton transfers take place are analyzed regarding their contribution to the efficiency of intramolecular processes through the assessment of effective molarities by DFT calculations on rigid intra-molecular model systems in comparison with their intermolecular counterparts. A few cyclic systems in which there is no possibility of hydrogen bonding between reactants neither in the ground state nor in the product are identified by theoretical calculations as leading to important rate increases in intramolecular general-base catalysis constituting a new exception to the rule of low effective molarities (EMs) for proton transfers. The recovery of high efficiency in these systems is attributed to the absence of special features facilitating the corresponding intermolecular reactions. This work confirms that any explanation of EMs found in intramolecular systems also requires a careful analysis of the corresponding bimolecular systems.
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Affiliation(s)
- Rafik Karaman
- Faculty of Pharmacy, Medicinal Chemistry, Al-Quds University, Main Campus, P.O. Box 20002, Abu-Dies, Jerusalem 20002, Palestine.
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Karaman R. A general equation correlating intramolecular rates with ‘attack’ parameters: distance and angle. Tetrahedron Lett 2010. [DOI: 10.1016/j.tetlet.2010.07.137] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Abstract
Density Functional Theory (DFT) and ab initio calculation results for the proton transfer reaction in Kirby's enzyme models 1-6 reveal that the reaction rate is largely dependent on the existence of a hydrogen bonding net in the reactants and the corresponding transition states. Further, the distance between the two reacting centers and the angle of the hydrogen bonding formed along the reaction path has profound effects on the rate. Hence, the study on the systems reported herein could provide a good basis for designing antimalarial (atovaquone) pro-drug systems that can be used to release the parent drug in a controlled manner. For example, based on the calculated log EM, the cleavage process for pro-drug 1Pro may be predicted to be about 10¹¹ times faster than that for a pro-drug 4Pro and about 10⁴ times faster than pro-drug 2Pro: rate (1Pro) > rate (2Pro > rate (4Pro). Thus, the rate by which the pro-drug releases the antimalarial drug can be determined according to the nature of the linker (Kirby's enzyme model 1-6).
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Affiliation(s)
- Rafik Karaman
- Faculty of Pharmacy, Al-Quds University, P. O. Box 20002, Jerusalem, Palestine.
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Affiliation(s)
- Rafik Karaman
- a Faculty of Pharmacy , Al-Quds University , P.O. Box 20002, Jerusalem, Palestine
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Karaman R. The effective molarity (EM)--a computational approach. Bioorg Chem 2010; 38:165-72. [PMID: 20451948 DOI: 10.1016/j.bioorg.2010.04.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2010] [Revised: 04/05/2010] [Accepted: 04/07/2010] [Indexed: 10/19/2022]
Abstract
The effective molarity (EM) for 12 intramolecular S(N)2 processes involving the formation of substituted aziridines and substituted epoxides were computed using ab initio and DFT calculation methods. Strong correlation was found between the calculated effective molarity and the experimentally determined values. This result could open a door for obtaining EM values for intramolecular processes that are difficult to be experimentally provided. Furthermore, the calculation results reveal that the driving forces for ring-closing reactions in the two different systems are proximity orientation of the nucleophile to the electrophile and the ground strain energies of the products and the reactants.
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Affiliation(s)
- Rafik Karaman
- Faculty of Pharmacy, Al-Quds University, P.O. Box 20002, Jerusalem, Palestine.
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Karaman R. The efficiency of proton transfer in Kirby’s enzyme model, a computational approach. Tetrahedron Lett 2010. [DOI: 10.1016/j.tetlet.2010.02.062] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Karaman R. Effects of substitution on the effective molarity (EM) for five membered ring-closure reactions – A computational approach. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.theochem.2009.09.035] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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The gem-disubstituent effect—a computational study that exposes the relevance of existing theoretical models. Tetrahedron Lett 2009. [DOI: 10.1016/j.tetlet.2009.08.072] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Karaman R. Cleavage of Menger’s aliphatic amide: A model for peptidase enzyme solely explained by proximity orientation in intramolecular proton transfer. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2009.06.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Karaman R. The effective molarity (EM) puzzle in proton transfer reactions. Bioorg Chem 2009; 37:106-10. [PMID: 19487010 DOI: 10.1016/j.bioorg.2009.04.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2009] [Revised: 03/24/2009] [Accepted: 04/24/2009] [Indexed: 11/24/2022]
Abstract
The DFT and HF calculation results for the proton transfer reactions of three different systems reveal that the reaction mechanism (transfer of a proton to a nucleophile) is largely determined by the distance between the two reactive centers (r). Systems with relatively large r values tend to abstract a proton from a molecule of water, whereas, these with a relatively small r values prefer to be engaged intramolecularly and their interaction with water is only via hydrogen bonding. Further, the results indicate that the effective molarity (logEM) for an intramolecular process is strongly correlated with the distance between the two reacting centers (r) in accordance with Menger's "spatiotemporal hypothesis".
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Affiliation(s)
- Rafik Karaman
- Faculty of Pharmacy, Al-Quds University, Jerusalem, Palestinian Territories.
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Accelerations in the Lactonization of Trimethyl Lock Systems Are due to Proximity Orientation and not to Strain Effects. ACTA ACUST UNITED AC 2009. [DOI: 10.1155/2009/240253] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
DFT at B3LYP/6-31G(d,p) and HF at 6-31G and AM1 semiempirical calculations of thermodynamc
and kinetic parameters for the trimethyl lock system (an important enzyme model) indicate that the
remarkable enhancement in the lactonizations is largely the result of a proximity orientation as opposed
to the currently advanced strain effect.
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Karaman R. A new mathematical equation relating activation energy to bond angle and distance: A key for understanding the role of acceleration in lactonization of the trimethyl lock system. Bioorg Chem 2008; 37:11-25. [PMID: 18952252 DOI: 10.1016/j.bioorg.2008.08.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2008] [Revised: 08/19/2008] [Accepted: 08/31/2008] [Indexed: 11/17/2022]
Abstract
AM1 semi-empirical molecular orbital and ab initio HF at the 6-31G level calculations for the lactonization processes of 12 different hydroxy acids (1a-1l) which differ in their structural features have been conducted. The calculations obtained reveal the following: (1) The rate-limiting step in the lactonization process is formation of a tetrahedral intermediate and not its collapse as was previously reported. (2) The rate-limiting step in both the acid-catalyzed and uncatalyzed lactonization is composed of two successive steps: approach of the hydroxyl toward the carbonyl carbon until it reaches a distance of 1.4 -1.5A, followed by proton transfer from the ether-type oxygen to one of the hydroxyls in the tetrahedral intermediate. Calculations of the activation energies for formation of the tetrahedral intermediate in the 12 hydroxy acids studied indicate: (1) A linear relationship exists between the change in enthalpic energy (E) and the ratio of the attack angle (nucleophilic-oxygen/carbonyl-carbon/alphalambdapietaalpha-carbon) to the distance (nucleophilic-oxygen/carbonyl-carbon) termed alpha/r; (2) The slope (S) of E vs. alpha/r plots depend on the nature of the hydroxy acids. Furthermore, plots of S values against the experimental rate values (log k(exp)) show a linear correlation with a high correlation coefficient. The combined results suggest that hydroxy acids with low S values have high k(exp) values due to enthalpic proximity effects.
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Affiliation(s)
- Rafik Karaman
- College of Pharmacy, Al-Quds University, Abu-Dies, Jerusalem, Palestinian Territory.
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