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Khan A, Khan SU, Khan A, Shal B, Rehman SU, Rehman SU, Htar TT, Khan S, Anwar S, Alafnan A, Rengasamy KRR. Anti-Inflammatory and Anti-Rheumatic Potential of Selective Plant Compounds by Targeting TLR-4/AP-1 Signaling: A Comprehensive Molecular Docking and Simulation Approaches. Molecules 2022; 27:molecules27134319. [PMID: 35807562 PMCID: PMC9268648 DOI: 10.3390/molecules27134319] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/23/2022] [Accepted: 06/29/2022] [Indexed: 11/16/2022] Open
Abstract
Plants are an important source of drug development and numerous plant derived molecules have been used in clinical practice for the ailment of various diseases. The Toll-like receptor-4 (TLR-4) signaling pathway plays a crucial role in inflammation including rheumatoid arthritis. The TLR-4 binds with pro-inflammatory ligands such as lipopolysaccharide (LPS) to induce the downstream signaling mechanism such as nuclear factor κappa B (NF-κB) and mitogen activated protein kinases (MAPKs). This signaling activation leads to the onset of various diseases including inflammation. In the present study, 22 natural compounds were studied against TLR-4/AP-1 signaling, which is implicated in the inflammatory process using a computational approach. These compounds belong to various classes such as methylxanthine, sesquiterpene lactone, alkaloid, flavone glycosides, lignan, phenolic acid, etc. The compounds exhibited different binding affinities with the TLR-4, JNK, NF-κB, and AP-1 protein due to the formation of multiple hydrophilic and hydrophobic interactions. With TLR-4, rutin had the highest binding energy (−10.4 kcal/mol), poncirin had the highest binding energy (−9.4 kcal/mol) with NF-κB and JNK (−9.5 kcal/mol), respectively, and icariin had the highest binding affinity (−9.1 kcal/mol) with the AP-1 protein. The root means square deviation (RMSD), root mean square fraction (RMSF), and radius of gyration (RoG) for 150 ns were calculated using molecular dynamic simulation (MD simulation) based on rutin’s greatest binding energy with TLR-4. The RMSD, RMSF, and RoG were all within acceptable limits in the MD simulation, and the complex remained stable for 150 ns. Furthermore, these compounds were assessed for the potential toxic effect on various organs such as the liver, heart, genotoxicity, and oral maximum toxic dose. Moreover, the blood–brain barrier permeability and intestinal absorption were also predicted using SwissADME software (Lausanne, Switzerland). These compounds exhibited promising physico-chemical as well as drug-likeness properties. Consequently, these selected compounds portray promising anti-inflammatory and drug-likeness properties.
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Affiliation(s)
- Ashrafullah Khan
- Pharmacological Sciences Research Lab, Department of Pharmacy, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan; (A.K.); (A.K.); (B.S.)
- Faculty of Pharmaceutical Sciences, Abasyn University, Peshawar 25000, Pakistan;
| | - Shafi Ullah Khan
- Faculty of Pharmaceutical Sciences, Abasyn University, Peshawar 25000, Pakistan;
- Product & Process Innovation Department, Qarshi Brands (Pvt) Ltd., Hattar 22610, Pakistan
| | - Adnan Khan
- Pharmacological Sciences Research Lab, Department of Pharmacy, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan; (A.K.); (A.K.); (B.S.)
| | - Bushra Shal
- Pharmacological Sciences Research Lab, Department of Pharmacy, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan; (A.K.); (A.K.); (B.S.)
- Faculty of Health Sciences, IQRA University, Islamabad Campus (Chak Shahzad), Park link Rd., Islamabad 44000, Pakistan
| | - Sabih Ur Rehman
- Department of Pharmacy, Forman Christian College (A Chartered University), Lahore 54600, Pakistan; (S.U.R.); (S.U.R.)
| | - Shaheed Ur Rehman
- Department of Pharmacy, Forman Christian College (A Chartered University), Lahore 54600, Pakistan; (S.U.R.); (S.U.R.)
| | - Thet Thet Htar
- School of Pharmacy, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Subang Jaya 47500, Selangor, Malaysia;
| | - Salman Khan
- Pharmacological Sciences Research Lab, Department of Pharmacy, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan; (A.K.); (A.K.); (B.S.)
- Correspondence: or (S.K.); (K.R.R.)
| | - Sirajudheen Anwar
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Hail, Hail 55211, Saudi Arabia; (S.A.); (A.A.)
| | - Ahmed Alafnan
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Hail, Hail 55211, Saudi Arabia; (S.A.); (A.A.)
| | - Kannan RR Rengasamy
- Center of Excellence for Pharmaceutical Sciences, North-West University, Potchefstroom 2520, South Africa
- Center for Transdisciplinary Research, Department of Pharmacology, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha Dental College, Chennai 600077, India
- Correspondence: or (S.K.); (K.R.R.)
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Markovic M, Ben-Shabat S, Nagendra Manda J, Abramov-Harpaz K, Regev C, Miller Y, Aponick A, Zimmermann EM, Dahan A. PLA 2-Triggered Activation of Cyclosporine-Phospholipid Prodrug as a Drug Targeting Approach in Inflammatory Bowel Disease Therapy. Pharmaceutics 2022; 14:pharmaceutics14030675. [PMID: 35336048 PMCID: PMC8950246 DOI: 10.3390/pharmaceutics14030675] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 03/13/2022] [Accepted: 03/15/2022] [Indexed: 02/04/2023] Open
Abstract
Oral medication with activity specifically at the inflamed sites throughout the gastrointestinal tract and limited systemic exposure would be a major advance in our therapeutic approach to inflammatory bowel disease (IBD). For this purpose, we have designed a prodrug by linking active drug moiety to phospholipid (PL), the substrate of phospholipase A2 (PLA2). PLA2 expression and activity is significantly elevated in the inflamed intestinal tissues of IBD patients. Since PLA2 enzyme specifically hydrolyses the sn-2 bond within PLs, in our PL-based prodrug approach, the sn-2 positioned FA is replaced with cyclosporine, so that PLA2 may be exploited as the prodrug-activating enzyme, releasing the free drug from the PL-complex. Owing to the enzyme overexpression, this may effectively target free cyclosporine to the sites of inflammation. Four PL-cyclosporine prodrugs were synthesized, differing by their linker length between the PL and the drug moiety. To study the prodrug activation, a novel enzymatically enriched model was developed, the colonic brush border membrane vesicles (cBBMVs); in this model, tissue vesicles were produced from colitis-induced (vs. healthy) rat colons. PLA2 overexpression (3.4-fold) was demonstrated in diseased vs. healthy cBBMVs. Indeed, while healthy cBBMVs induced only marginal activation, substantial prodrug activation was evident by colitis-derived cBBMVs. Together with the PLA2 overexpression, these data validate our drug targeting strategy. In the diseased cBBMVs, quick and complete activation of the entire dose was obtained for the 12-carbon linker prodrug, while slow and marginal activation was obtained for the 6/8-carbon linkers. The potential to target the actual sites of inflammation and treat any localizations throughout the GIT, together with the extended therapeutic index, makes this orally delivered prodrug approach an exciting new therapeutic strategy for IBD treatment.
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Affiliation(s)
- Milica Markovic
- Department of Clinical Pharmacology, School of Pharmacy, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel; (M.M.); (S.B.-S.)
| | - Shimon Ben-Shabat
- Department of Clinical Pharmacology, School of Pharmacy, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel; (M.M.); (S.B.-S.)
| | | | - Karina Abramov-Harpaz
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel; (K.A.-H.); (C.R.); (Y.M.)
- Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Clil Regev
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel; (K.A.-H.); (C.R.); (Y.M.)
- Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Yifat Miller
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel; (K.A.-H.); (C.R.); (Y.M.)
- Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Aaron Aponick
- Department of Chemistry, University of Florida, Gainesville, FL 32603, USA; (J.N.M.); (A.A.)
| | - Ellen M. Zimmermann
- Department of Medicine, Division of Gastroenterology, University of Florida, Gainesville, FL 32610, USA;
| | - Arik Dahan
- Department of Clinical Pharmacology, School of Pharmacy, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel; (M.M.); (S.B.-S.)
- Correspondence:
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3
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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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Markovic M, Ben-Shabat S, Dahan A. Prodrugs for Improved Drug Delivery: Lessons Learned from Recently Developed and Marketed Products. Pharmaceutics 2020; 12:pharmaceutics12111031. [PMID: 33137942 PMCID: PMC7692606 DOI: 10.3390/pharmaceutics12111031] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/18/2020] [Accepted: 10/23/2020] [Indexed: 12/18/2022] Open
Abstract
Prodrugs are bioreversible, inactive drug derivatives, which have the ability to convert into a parent drug in the body. In the past, prodrugs were used as a last option; however, nowadays, prodrugs are considered already in the early stages of drug development. Optimal prodrug needs to have effective absorption, distribution, metabolism, and elimination (ADME) features to be chemically stable, to be selective towards the particular site in the body, and to have appropriate safety. Traditional prodrug approach aims to improve physicochemical/biopharmaceutical drug properties; modern prodrugs also include cellular and molecular parameters to accomplish desired drug effect and site-specificity. Here, we present recently investigated prodrugs, their pharmaceutical and clinical advantages, and challenges facing the overall prodrug development. Given examples illustrate that prodrugs can accomplish appropriate solubility, increase permeability, provide site-specific targeting (i.e., to organs, tissues, enzymes, or transporters), overcome rapid drug metabolism, decrease toxicity, or provide better patient compliance, all with the aim to provide optimal drug therapy and outcome. Overall, the prodrug approach is a powerful tool to decrease the time/costs of developing new drug entities and improve overall drug therapy.
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Affiliation(s)
| | | | - Arik Dahan
- Correspondence: ; Tel.: +972-8-6479483; Fax: +972-8-6479303
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Markovic M, Ben-Shabat S, Dahan A. Computational Simulations to Guide Enzyme-Mediated Prodrug Activation. Int J Mol Sci 2020; 21:ijms21103621. [PMID: 32443905 PMCID: PMC7279318 DOI: 10.3390/ijms21103621] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 12/13/2022] Open
Abstract
Prodrugs are designed to improve pharmaceutical/biopharmaceutical characteristics, pharmacokinetic/pharmacodynamic properties, site-specificity, and more. A crucial step in successful prodrug is its activation, which releases the active parent drug, exerting a therapeutic effect. Prodrug activation can be based on oxidation/reduction processes, or through enzyme-mediated hydrolysis, from oxidoreductases (i.e., Cytochrome P450) to hydrolytic enzymes (i.e., carboxylesterase). This study provides an overview of the novel in silico methods for the optimization of enzyme-mediated prodrug activation. Computational methods simulating enzyme-substrate binding can be simpler like molecular docking, or more complex, such as quantum mechanics (QM), molecular mechanics (MM), and free energy perturbation (FEP) methods such as molecular dynamics (MD). Examples for MD simulations used for elucidating the mechanism of prodrug (losartan, paclitaxel derivatives) metabolism via CYP450 enzyme are presented, as well as an MD simulation for optimizing linker length in phospholipid-based prodrugs. Molecular docking investigating quinazolinone prodrugs as substrates for alkaline phosphatase is also presented, as well as QM and MD simulations used for optimal fit of different prodrugs within the human carboxylesterase 1 catalytical site. Overall, high quality computational simulations may show good agreement with experimental results, and should be used early in the prodrug development process.
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Markovic M, Ben-Shabat S, Aponick A, Zimmermann EM, Dahan A. Lipids and Lipid-Processing Pathways in Drug Delivery and Therapeutics. Int J Mol Sci 2020; 21:ijms21093248. [PMID: 32375338 PMCID: PMC7247327 DOI: 10.3390/ijms21093248] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 04/28/2020] [Accepted: 05/02/2020] [Indexed: 12/19/2022] Open
Abstract
The aim of this work is to analyze relevant endogenous lipid processing pathways, in the context of the impact that lipids have on drug absorption, their therapeutic use, and utilization in drug delivery. Lipids may serve as biomarkers of some diseases, but they can also provide endogenous therapeutic effects for certain pathological conditions. Current uses and possible clinical benefits of various lipids (fatty acids, steroids, triglycerides, and phospholipids) in cancer, infectious, inflammatory, and neurodegenerative diseases are presented. Lipids can also be conjugated to a drug molecule, accomplishing numerous potential benefits, one being the improved treatment effect, due to joined influence of the lipid carrier and the drug moiety. In addition, such conjugates have increased lipophilicity relative to the parent drug. This leads to improved drug pharmacokinetics and bioavailability, the ability to join endogenous lipid pathways and achieve drug targeting to the lymphatics, inflamed tissues in certain autoimmune diseases, or enable overcoming different barriers in the body. Altogether, novel mechanisms of the lipid role in diseases are constantly discovered, and new ways to exploit these mechanisms for the optimal drug design that would advance different drug delivery/therapy aspects are continuously emerging.
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Affiliation(s)
- Milica Markovic
- Department of Clinical Pharmacology, School of Pharmacy, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel; (M.M.); (S.B.-S.)
| | - Shimon Ben-Shabat
- Department of Clinical Pharmacology, School of Pharmacy, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel; (M.M.); (S.B.-S.)
| | - Aaron Aponick
- Department of Chemistry, University of Florida, Gainesville, FL 32603, USA;
| | - Ellen M. Zimmermann
- Department of Medicine, Division of Gastroenterology, University of Florida, Gainesville, FL 32610, USA;
| | - Arik Dahan
- Department of Clinical Pharmacology, School of Pharmacy, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel; (M.M.); (S.B.-S.)
- Correspondence:
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The prospects of lipidic prodrugs: an old approach with an emerging future. Future Med Chem 2019; 11:2563-2571. [DOI: 10.4155/fmc-2019-0155] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Nowadays, prodrugs are no longer used as a last resort, rather, they are intentionally designed at the early stages of drug development. Lipidic prodrug strategy, where a drug moiety is covalently bound to a lipid carrier, was initially proposed half a century ago, yet, this approach still remains to be explored. Lipidic prodrugs can join physiological lipid metabolic pathways, and hence provide drug targeting via lymphatic transport or site-specific drug release, improve drugs’ pharmacokinetic profile, overcome obstacles originating from biological barriers and bypass hepatic first-pass metabolism. Physiological pathways of lipid processing, uses of different lipidic prodrugs and their clinical benefits are overviewed. Overall, lipidic prodrugs present a promising approach for overcoming different obstacles and fulfilling various unmet needs in drug delivery/targeting.
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8
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Markovic M, Ben-Shabat S, Keinan S, Aponick A, Zimmermann EM, Dahan A. Molecular Modeling-Guided Design of Phospholipid-Based Prodrugs. Int J Mol Sci 2019; 20:ijms20092210. [PMID: 31060339 PMCID: PMC6538990 DOI: 10.3390/ijms20092210] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 04/29/2019] [Accepted: 05/01/2019] [Indexed: 02/06/2023] Open
Abstract
The lipidic prodrug approach is an emerging field for improving a number of biopharmaceutical and drug delivery aspects. Owing to their structure and nature, phospholipid (PL)-based prodrugs may join endogenous lipid processing pathways, and hence significantly improve the pharmacokinetics and/or bioavailability of the drug. Additional advantages of this approach include drug targeting by enzyme-triggered drug release, blood–brain barrier permeability, lymphatic targeting, overcoming drug resistance, or enabling appropriate formulation. The PL-prodrug design includes various structural modalities-different conjugation strategies and/or the use of linkers between the PL and the drug moiety, which considerably influence the prodrug characteristics and the consequent effects. In this article, we describe how molecular modeling can guide the structural design of PL-based prodrugs. Computational simulations can predict the extent of phospholipase A2 (PLA2)-mediated activation, and facilitate prodrug development. Several computational methods have been used to facilitate the design of the pro-drugs, which will be reviewed here, including molecular docking, the free energy perturbation method, molecular dynamics simulations, and free density functional theory. Altogether, the studies described in this article indicate that computational simulation-guided PL-based prodrug molecular design correlates well with the experimental results, allowing for more mechanistic and less empirical development. In the future, the use of molecular modeling techniques to predict the activity of PL-prodrugs should be used earlier in the development process.
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Affiliation(s)
- Milica Markovic
- Department of Clinical Pharmacology, School of Pharmacy, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel.
| | - Shimon Ben-Shabat
- Department of Clinical Pharmacology, School of Pharmacy, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel.
| | | | - Aaron Aponick
- Department of Chemistry, University of Florida, Gainesville, FL 32603, USA.
| | - Ellen M Zimmermann
- Department of Medicine, Division of Gastroenterology, University of Florida, Gainesville, FL 32608, USA.
| | - Arik Dahan
- Department of Clinical Pharmacology, School of Pharmacy, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel.
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Markovic M, Dahan A, Keinan S, Kurnikov I, Aponick A, Zimmermann EM, Ben-Shabat S. Phospholipid-Based Prodrugs for Colon-Targeted Drug Delivery: Experimental Study and In-Silico Simulations. Pharmaceutics 2019; 11:pharmaceutics11040186. [PMID: 30995772 PMCID: PMC6523355 DOI: 10.3390/pharmaceutics11040186] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/07/2019] [Accepted: 04/08/2019] [Indexed: 12/23/2022] Open
Abstract
In ulcerative colitis (UC), the inflammation is localized in the colon, and one of the successful strategies for colon-targeting drug delivery is the prodrug approach. In this work, we present a novel phospholipid (PL)-based prodrug approach, as a tool for colonic drug targeting in UC. We aim to use the phospholipase A2 (PLA2), an enzyme that is overexpressed in the inflamed colonic tissues of UC patients, as the PL-prodrug activating enzyme, to accomplish the liberation of the parent drug from the prodrug complex at the specific diseased tissue(s). Different linker lengths between the PL and the drug moiety can dictate the rate of activation by PLA2, and subsequently determine the amount of free drugs at the site of action. The feasibility of this approach was studied with newly synthesized PL-Fmoc (fluorenylmethyloxycarbonyl) conjugates, using Fmoc as a model compound for testing our hypothesis. In vitro incubation with bee venom PLA2 demonstrated that a 7-carbon linker between the PL and Fmoc has higher activation rate than a 5-carbon linker. 4-fold higher colonic expression of PLA2 was demonstrated in colonic mucosa of colitis-induced rats when compared to healthy animals, validating our hypothesis of a colitis-targeting prodrug approach. Next, a novel molecular dynamics (MD) simulation was developed for PL-based prodrugs containing clinically relevant drugs. PL-methotrexate conjugate with 6-carbon linker showed the highest extent of PLA2-mediated activation, whereas shorter linkers were activated to a lower extent. In conclusion, this work demonstrates that for carefully designed PL-drug conjugates, PLA2 overexpression in inflamed colonic tissues can be used as prodrug-activating enzyme and drug targeting strategy, including insights into the activation mechanisms in a PLA2 binding site.
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Affiliation(s)
- Milica Markovic
- Department of Clinical Pharmacology, School of Pharmacy, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel.
| | - Arik Dahan
- Department of Clinical Pharmacology, School of Pharmacy, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel.
| | | | | | - Aaron Aponick
- Department of Chemistry, University of Florida, Gainesville, FL 32603, USA.
| | - Ellen M Zimmermann
- Department of Medicine, Division of Gastroenterology, University of Florida, Gainesville, FL 32603, USA.
| | - Shimon Ben-Shabat
- Department of Clinical Pharmacology, School of Pharmacy, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel.
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10
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Ngo ST, Vu KB, Bui LM, Vu VV. Effective Estimation of Ligand-Binding Affinity Using Biased Sampling Method. ACS OMEGA 2019; 4:3887-3893. [PMID: 31459599 PMCID: PMC6648447 DOI: 10.1021/acsomega.8b03258] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 02/08/2019] [Indexed: 05/09/2023]
Abstract
The binding between two biomolecules is one of the most critical factors controlling many bioprocesses. Therefore, it is of great interest to derive a reliable method to calculate the free binding energy between two biomolecules. In this work, we have demonstrated that the binding affinity of ligands to proteins can be determined through biased sampling simulations. The umbrella sampling (US) method was applied on 20 protein-ligand complexes, including the cathepsin K (CTSK), type II dehydroquinase (DHQase), heat shock protein 90 (HSP90), and factor Xa (FXa) systems. The ligand-binding affinity was evaluated as the difference between the largest and smallest values of the free-energy curve, which was obtained via a potential of mean force analysis. The calculated affinities differ sizably from the previously reported experimental values, with an average difference of ∼3.14 kcal/mol. However, the calculated results are in good correlation with the experimental data, with correlation coefficients of 0.76, 0.87, 0.96, and 0.97 for CTSK, DHQase, HSP90, and FXa, respectively. Thus, the binding free energy of a new ligand can be reliably estimated using our US approach. Furthermore, the root-mean-square errors (RMSEs) of binding affinity of these systems are 1.13, 0.90, 0.37, and 0.25 kcal/mol, for CTSK, DHQase, HSP90, and FXa, respectively. The small RMSE values indicate the good precision of the biased sampling method that can distinguish the ligands exhibiting similar binding affinities.
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Affiliation(s)
- Son Tung Ngo
- Laboratory of Theoretical
and Computational Biophysics, Ton Duc Thang
University, Ho Chi Minh City 7000000, Vietnam
- Faculty
of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City 7000000, Vietnam
| | - Khanh B. Vu
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City 700000, Vietnam
| | - Le Minh Bui
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City 700000, Vietnam
| | - Van V. Vu
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City 700000, Vietnam
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11
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Markovic M, Ben-Shabat S, Keinan S, Aponick A, Zimmermann EM, Dahan A. Prospects and Challenges of Phospholipid-Based Prodrugs. Pharmaceutics 2018; 10:pharmaceutics10040210. [PMID: 30388756 PMCID: PMC6321354 DOI: 10.3390/pharmaceutics10040210] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 10/24/2018] [Accepted: 10/26/2018] [Indexed: 12/19/2022] Open
Abstract
Nowadays, the prodrug approach is used already at the early stages of drug development. Lipidic prodrug approach is a growing field for improving a number of drug properties/delivery/therapy aspects, and can offer solutions for various unmet needs. This approach includes drug moiety bound to the lipid carrier, which can be triglyceride, fatty acids, steroid, or phospholipid (PL). The focus of this article is PL-based prodrugs, which includes a PL carrier covalently bound to the active drug moiety. An overview of relevant physiological lipid processing pathways and absorption barriers is provided, followed by drug delivery/therapeutic application of PL-drug conjugates, as well as computational modeling techniques, and a modern bioinformatics tool that can aid in the optimization of PL conjugates. PL-based prodrugs have increased lipophilicity comparing to the parent drug, and can therefore significantly improve the pharmacokinetic profile and overall bioavailability of the parent drug, join the endogenous lipid processing pathways and therefore accomplish drug targeting, e.g., by lymphatic transport, drug release at specific target site(s), or passing the blood-brain barrier. Moreover, an exciting gateway for treating inflammatory diseases and cancer is presented, by utilizing the PL sn-2 position in the prodrug design, aiming for PLA₂-mediated activation. Overall, a PL-based prodrug approach shows great potential in improving different drug delivery/therapy aspects, and is expected to grow.
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Affiliation(s)
- Milica Markovic
- Department of Clinical Pharmacology, School of Pharmacy, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel.
| | - Shimon Ben-Shabat
- Department of Clinical Pharmacology, School of Pharmacy, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel.
| | | | - Aaron Aponick
- Department of Chemistry, University of Florida, Gainesville, FL 32603, USA.
| | - Ellen M Zimmermann
- Department of Medicine, Division of Gastroenterology, University of Florida, Gainesville, FL 32610, USA.
| | - Arik Dahan
- Department of Clinical Pharmacology, School of Pharmacy, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel.
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Markovic M, Ben‐Shabat S, Keinan S, Aponick A, Zimmermann EM, Dahan A. Lipidic prodrug approach for improved oral drug delivery and therapy. Med Res Rev 2018; 39:579-607. [DOI: 10.1002/med.21533] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 07/26/2018] [Accepted: 07/27/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Milica Markovic
- Department of Clinical PharmacologySchool of Pharmacy, Faculty of Health Sciences, Ben‐Gurion University of the NegevBeer‐Sheva Israel
| | - Shimon Ben‐Shabat
- Department of Clinical PharmacologySchool of Pharmacy, Faculty of Health Sciences, Ben‐Gurion University of the NegevBeer‐Sheva Israel
| | | | - Aaron Aponick
- Department of ChemistryUniversity of FloridaGainesville Florida
| | - Ellen M. Zimmermann
- Department of MedicineDivision of Gastroenterology, University of FloridaGainesville Florida
| | - Arik Dahan
- Department of Clinical PharmacologySchool of Pharmacy, Faculty of Health Sciences, Ben‐Gurion University of the NegevBeer‐Sheva Israel
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Keinan S, Hatcher Frush E, Shipman WJ. Leveraging Cloud Computing for In-Silico Drug Design Using the Quantum Molecular Design (QMD) Framework. Comput Sci Eng 2018. [DOI: 10.1109/mcse.2018.042781327] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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