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Zajda A, Sikora J, Hynninen M, Tampio J, Huttunen KM, Markowicz-Piasecka M. Substituent effects of sulfonamide derivatives of metformin that can dually improve cellular glucose utilization and anti-coagulation. Chem Biol Interact 2023; 373:110381. [PMID: 36746201 DOI: 10.1016/j.cbi.2023.110381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 02/03/2023] [Indexed: 02/07/2023]
Abstract
Metformin, the most frequently prescribed medicine for the management of type 2 diabetes, has been shown to reduce cardiovascular events in diabetic patients in pre-clinical and clinical studies. The present work reports the design, synthesis, and biological assessment of the impact of six benzenesulfonamide biguanides on various aspects of hemostasis, cell function, red blood cell integrity (RBC), and their ability to uptake glucose in human umbilical endothelial cells (HUVECs). It was found that all synthesized o- and m-benzenesulfonamides, particularly derivatives with nitro (3) and amino groups (4), are characterized by a good safety profile in HUVECs, which was further confirmed in the cellular integrity studies. The biguanide analogues with methoxy group (1, 2) and an amino substituent (5, 6) significantly increased glucose utilization in HUVECs, similarly to the parent drug. Intriguingly, compounds 1, 3, and 6 favourably influenced some of the coagulation parameters. Furthermore, derivative 3 also slowed the process of fibrin polymerization, indicating more beneficial anti-coagulant properties than metformin. None of the novel metformin analogues interact strongly with the erythrocyte lipid-protein bilayer. Our findings indicate that derivative 3 has highly desirable anti-coagulant properties, and compounds 1 and 6 have potential dual-action activity, including anti-hyperglycaemic properties and anti-coagulant activity. As such, these derivatives can be used as lead molecules for further development of anti-diabetic agents with a beneficial effect on hypercoagulability.
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Affiliation(s)
- Agnieszka Zajda
- Laboratory of Bioanalysis, Department of Pharmaceutical Chemistry, Drug Analysis and Radiopharmacy, Medical University of Lodz, ul. Muszyńskiego1, 90-151, Lodz, Poland.
| | - Joanna Sikora
- Department of Bioinorganic Chemistry, Medical University of Lodz, ul. Muszyńskiego1, 90-151, Lodz, Poland.
| | - Mira Hynninen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Yliopistonranta 1C, P.O. Box 1627, 70211, Kuopio, Finland.
| | - Janne Tampio
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Yliopistonranta 1C, P.O. Box 1627, 70211, Kuopio, Finland.
| | - Kristiina M Huttunen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Yliopistonranta 1C, P.O. Box 1627, 70211, Kuopio, Finland.
| | - Magdalena Markowicz-Piasecka
- Laboratory of Bioanalysis, Department of Pharmaceutical Chemistry, Drug Analysis and Radiopharmacy, Medical University of Lodz, ul. Muszyńskiego1, 90-151, Lodz, Poland.
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2
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Antipin IS, Alfimov MV, Arslanov VV, Burilov VA, Vatsadze SZ, Voloshin YZ, Volcho KP, Gorbatchuk VV, Gorbunova YG, Gromov SP, Dudkin SV, Zaitsev SY, Zakharova LY, Ziganshin MA, Zolotukhina AV, Kalinina MA, Karakhanov EA, Kashapov RR, Koifman OI, Konovalov AI, Korenev VS, Maksimov AL, Mamardashvili NZ, Mamardashvili GM, Martynov AG, Mustafina AR, Nugmanov RI, Ovsyannikov AS, Padnya PL, Potapov AS, Selektor SL, Sokolov MN, Solovieva SE, Stoikov II, Stuzhin PA, Suslov EV, Ushakov EN, Fedin VP, Fedorenko SV, Fedorova OA, Fedorov YV, Chvalun SN, Tsivadze AY, Shtykov SN, Shurpik DN, Shcherbina MA, Yakimova LS. Functional supramolecular systems: design and applications. RUSSIAN CHEMICAL REVIEWS 2021. [DOI: 10.1070/rcr5011] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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3
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Abramyan TM, An Y, Kireev D. Off-Pocket Activity Cliffs: A Puzzling Facet of Molecular Recognition. J Chem Inf Model 2019; 60:152-161. [PMID: 31790251 DOI: 10.1021/acs.jcim.9b00731] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
While accurate quantitative prediction of ligand-protein binding affinity remains an elusive goal, high-affinity ligands to therapeutic targets are being designed through heuristic optimization of ligand-protein contacts. However, herein, through large-scale data mining and analyses, we demonstrate that a ligand's binding can also be strongly affected through modifying its solvent-exposed portion that does not make contacts with the protein, thus resulting in "off-pocket activity cliffs" (OAC). We then exposed the roots of the OAC phenomenon by means of molecular dynamics (MD) simulations and MD data analyses. We expect OAC to extend our knowledge of molecular recognition and enhance the drug designer's toolkit.
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Affiliation(s)
- Tigran M Abramyan
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina , 27599-7363
| | - Yi An
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina , 27599-7363
| | - Dmitri Kireev
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina , 27599-7363
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4
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Hao X, Zuo X, Kang D, Zhang J, Song Y, Liu X, Zhan P. Contemporary medicinal-chemistry strategies for discovery of blood coagulation factor Xa inhibitors. Expert Opin Drug Discov 2019; 14:915-931. [DOI: 10.1080/17460441.2019.1626821] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Xia Hao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Ji’nan, Shandong, PR China
| | - Xiaofang Zuo
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Ji’nan, Shandong, PR China
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Ji’nan, Shandong, PR China
| | - Jian Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Ji’nan, Shandong, PR China
| | - Yuning Song
- Department of Clinical Pharmacy, Qilu Hospital of Shandong University, Jinan, China
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Ji’nan, Shandong, PR China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Ji’nan, Shandong, PR China
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Patel NR, Patel DV, Kanhed AM, Patel SP, Patel KV, Afosah DK, Desai UR, Karpoormath R, Yadav MR. 2-Aminobenzamide-Based Factor Xa Inhibitors with Novel Mono- and Bi-Aryls as S4 Binding Elements. ChemistrySelect 2019. [DOI: 10.1002/slct.201803342] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Nirav R. Patel
- Faculty of Pharmacy; Kalabhavan Campus; The Maharaja Sayajirao University of Baroda, Vadodara-; 390001 Gujarat India
| | - Dushyant V. Patel
- Faculty of Pharmacy; Kalabhavan Campus; The Maharaja Sayajirao University of Baroda, Vadodara-; 390001 Gujarat India
| | - Ashish M. Kanhed
- Faculty of Pharmacy; Kalabhavan Campus; The Maharaja Sayajirao University of Baroda, Vadodara-; 390001 Gujarat India
- Department of Pharmaceutical Chemistry; Discipline of Pharmaceutical Sciences; College of Health Sciences; University of KwaZulu-Natal (Westville); Durban 4000 South Africa
| | - Sagar P. Patel
- Faculty of Pharmacy; Kalabhavan Campus; The Maharaja Sayajirao University of Baroda, Vadodara-; 390001 Gujarat India
| | - Kirti V. Patel
- Faculty of Pharmacy; Kalabhavan Campus; The Maharaja Sayajirao University of Baroda, Vadodara-; 390001 Gujarat India
| | - Daniel K. Afosah
- Department of Medicinal Chemistry and Institute for Structrural Biology and Drug Discovery; Virginia Commonwealth University, Richmond; Virginia 23219 United States
| | - Umesh R. Desai
- Department of Medicinal Chemistry and Institute for Structrural Biology and Drug Discovery; Virginia Commonwealth University, Richmond; Virginia 23219 United States
| | - Rajshekhar Karpoormath
- Department of Pharmaceutical Chemistry; Discipline of Pharmaceutical Sciences; College of Health Sciences; University of KwaZulu-Natal (Westville); Durban 4000 South Africa
| | - Mange Ram Yadav
- Faculty of Pharmacy; Kalabhavan Campus; The Maharaja Sayajirao University of Baroda, Vadodara-; 390001 Gujarat India
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6
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Al-Horani RA, Afosah DK. Recent advances in the discovery and development of factor XI/XIa inhibitors. Med Res Rev 2018; 38:1974-2023. [PMID: 29727017 PMCID: PMC6173998 DOI: 10.1002/med.21503] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Revised: 03/09/2018] [Accepted: 04/04/2018] [Indexed: 12/12/2022]
Abstract
Factor XIa (FXIa) is a serine protease homodimer that belongs to the intrinsic coagulation pathway. FXIa primarily catalyzes factor IX activation to factor IXa, which subsequently activates factor X to factor Xa in the common coagulation pathway. Growing evidence suggests that FXIa plays an important role in thrombosis with a relatively limited contribution to hemostasis. Therefore, inhibitors targeting factor XI (FXI)/FXIa system have emerged as a paradigm-shifting strategy so as to develop a new generation of anticoagulants to effectively prevent and/or treat thromboembolic diseases without the life-threatening risk of internal bleeding. Several inhibitors of FXI/FXIa proteins have been discovered or designed over the last decade including polypeptides, active site peptidomimetic inhibitors, allosteric inhibitors, antibodies, and aptamers. Antisense oligonucleotides (ASOs), which ultimately reduce the hepatic biosynthesis of FXI, have also been introduced. A phase II study, which included patients undergoing elective primary unilateral total knee arthroplasty, revealed that a specific FXI ASO effectively protects patients against venous thrombosis with a relatively limited risk of bleeding. Initial findings have also demonstrated the potential of FXI/FXIa inhibitors in sepsis, listeriosis, and arterial hypertension. This review highlights various chemical, biochemical, and pharmacological aspects of FXI/FXIa inhibitors with the goal of advancing their development toward clinical use.
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Affiliation(s)
- Rami A. Al-Horani
- Division of Basic Pharmaceutical Sciences, College of Pharmacy, Xavier University of Louisiana, New Orleans, Louisiana 70125
| | - Daniel K. Afosah
- Department of Medicinal Chemistry and Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219
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Moriarty NW, Liebschner D, Klei HE, Echols N, Afonine PV, Headd JJ, Poon BK, Adams PD. Interactive comparison and remediation of collections of macromolecular structures. Protein Sci 2017; 27:182-194. [PMID: 28901593 DOI: 10.1002/pro.3296] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 09/08/2017] [Accepted: 09/11/2017] [Indexed: 11/09/2022]
Abstract
Often similar structures need to be compared to reveal local differences throughout the entire model or between related copies within the model. Therefore, a program to compare multiple structures and enable correction any differences not supported by the density map was written within the Phenix framework (Adams et al., Acta Cryst 2010; D66:213-221). This program, called Structure Comparison, can also be used for structures with multiple copies of the same protein chain in the asymmetric unit, that is, as a result of non-crystallographic symmetry (NCS). Structure Comparison was designed to interface with Coot(Emsley et al., Acta Cryst 2010; D66:486-501) and PyMOL(DeLano, PyMOL 0.99; 2002) to facilitate comparison of large numbers of related structures. Structure Comparison analyzes collections of protein structures using several metrics, such as the rotamer conformation of equivalent residues, displays the results in tabular form and allows superimposed protein chains and density maps to be quickly inspected and edited (via the tools in Coot) for consistency, completeness and correctness.
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Affiliation(s)
- Nigel W Moriarty
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Dorothee Liebschner
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Herbert E Klei
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Nathaniel Echols
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Pavel V Afonine
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jeffrey J Headd
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Billy K Poon
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Paul D Adams
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Bioengineering, University of California at Berkeley, Berkeley, CA, 94720, USA
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Wang Y, Sun X, Yang D, Guo Z, Fan X, Nie M, Zhang F, Liu Y, Li Y, Wang Y, Gong P, Liu Y. Design, synthesis, and structure–activity relationship of novel and effective apixaban derivatives as FXa inhibitors containing 1,2,4-triazole/pyrrole derivatives as P2 binding element. Bioorg Med Chem 2016; 24:5646-5661. [DOI: 10.1016/j.bmc.2016.09.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 09/09/2016] [Accepted: 09/10/2016] [Indexed: 11/24/2022]
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9
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Patel NR, Patel DV, Murumkar PR, Yadav MR. Contemporary developments in the discovery of selective factor Xa inhibitors: A review. Eur J Med Chem 2016; 121:671-698. [PMID: 27322757 DOI: 10.1016/j.ejmech.2016.05.039] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 04/25/2016] [Accepted: 05/19/2016] [Indexed: 11/25/2022]
Abstract
Thrombosis is a leading cause of death in cardiovascular diseases such as myocardial infarction (MI), unstable angina and acute coronary syndrome (ACS) in the industrialized world. Venous thromboembolism is observed in about 1 million people every year in United States causing significant morbidity and mortality. Conventional antithrombotic therapy has been reported to have several disadvantages and limitations like inconvenience in oral administration, bleeding risks (heparin analogs), narrow therapeutic window and undesirable interactions with food and drugs (vitamin K antagonist-warfarin). The unmet medical demand for orally active safe anticoagulants has generated widespread interest among the medicinal chemists engaged in this field. To modulate blood coagulation, various enzymes involved in the coagulation process have received great attention as potential targets by various research groups for the development of oral anticoagulants. Among these enzymes, factor Xa (FXa) has remained the centre of attention in the last decade. Intensive research efforts have been made by various research groups for the development of small, safe and orally bioavailable FXa inhibitors. This review is an attempt to compile the research work of various researchers in the direction of development of FXa inhibitors reported since 2010 onward.
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Affiliation(s)
- Nirav R Patel
- Faculty of Pharmacy, Kalabhavan Campus, The Maharaja Sayajirao University of Baroda, Vadodara 390001, Gujarat, India
| | - Dushyant V Patel
- Faculty of Pharmacy, Kalabhavan Campus, The Maharaja Sayajirao University of Baroda, Vadodara 390001, Gujarat, India
| | - Prashant R Murumkar
- Faculty of Pharmacy, Kalabhavan Campus, The Maharaja Sayajirao University of Baroda, Vadodara 390001, Gujarat, India
| | - Mange Ram Yadav
- Faculty of Pharmacy, Kalabhavan Campus, The Maharaja Sayajirao University of Baroda, Vadodara 390001, Gujarat, India.
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Rouden J, Lasne MC, Blanchet J, Baudoux J. (−)-Cytisine and Derivatives: Synthesis, Reactivity, and Applications. Chem Rev 2013; 114:712-78. [DOI: 10.1021/cr400307e] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Jacques Rouden
- Laboratoire de Chimie Moléculaire
et Thioorganique, ENSICAEN-Université de Caen, CNRS, Institut Normand de Chimie Moléculaire, Médicinale et Macromoléculaire (INC3M), 6 Boulevard du Maréchal Juin, 14050 Caen, France
| | - Marie-Claire Lasne
- Laboratoire de Chimie Moléculaire
et Thioorganique, ENSICAEN-Université de Caen, CNRS, Institut Normand de Chimie Moléculaire, Médicinale et Macromoléculaire (INC3M), 6 Boulevard du Maréchal Juin, 14050 Caen, France
| | - Jérôme Blanchet
- Laboratoire de Chimie Moléculaire
et Thioorganique, ENSICAEN-Université de Caen, CNRS, Institut Normand de Chimie Moléculaire, Médicinale et Macromoléculaire (INC3M), 6 Boulevard du Maréchal Juin, 14050 Caen, France
| | - Jérôme Baudoux
- Laboratoire de Chimie Moléculaire
et Thioorganique, ENSICAEN-Université de Caen, CNRS, Institut Normand de Chimie Moléculaire, Médicinale et Macromoléculaire (INC3M), 6 Boulevard du Maréchal Juin, 14050 Caen, France
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Liu S, Wu Y, Lin T, Abel R, Redmann JP, Summa CM, Jaber VR, Lim NM, Mobley DL. Lead optimization mapper: automating free energy calculations for lead optimization. J Comput Aided Mol Des 2013; 27:755-70. [PMID: 24072356 DOI: 10.1007/s10822-013-9678-y] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 09/04/2013] [Indexed: 01/31/2023]
Abstract
Alchemical free energy calculations hold increasing promise as an aid to drug discovery efforts. However, applications of these techniques in discovery projects have been relatively few, partly because of the difficulty of planning and setting up calculations. Here, we introduce lead optimization mapper, LOMAP, an automated algorithm to plan efficient relative free energy calculations between potential ligands within a substantial library of perhaps hundreds of compounds. In this approach, ligands are first grouped by structural similarity primarily based on the size of a (loosely defined) maximal common substructure, and then calculations are planned within and between sets of structurally related compounds. An emphasis is placed on ensuring that relative free energies can be obtained between any pair of compounds without combining the results of too many different relative free energy calculations (to avoid accumulation of error) and by providing some redundancy to allow for the possibility of error and consistency checking and provide some insight into when results can be expected to be unreliable. The algorithm is discussed in detail and a Python implementation, based on both Schrödinger's and OpenEye's APIs, has been made available freely under the BSD license.
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Affiliation(s)
- Shuai Liu
- Department of Pharmaceutical Sciences and Department of Chemistry, University of California, Irvine, 147 Bison Modular, Irvine, CA, 92697, USA
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