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Sun L, Wang Z, Yang Z, Liu X, Dong H. Virtual screening and structure-activity relationship study of novel BTK inhibitors in Traditional Chinese Medicine for the treatment of rheumatoid arthritis. J Biomol Struct Dyn 2023; 41:15219-15233. [PMID: 36914235 DOI: 10.1080/07391102.2023.2188418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 02/26/2023] [Indexed: 03/14/2023]
Abstract
Bruton tyrosine kinase (BTK) is a known drug target for the treatment of autoimmune diseases, including rheumatoid arthritis (RA). In this study, a series of 1-amino-1H-imidazole-5-carboxamide derivatives with good inhibitory activity against BTK were selected to explore the structure-activity relationships of these BTK inhibitors (BTKIs). Furthermore, we concentrated on 182 prescriptions of Traditional Chinese Medicine with therapeutic effects on RA. 54 herbs with a frequency of ≥10 were counted to establish a database containing 4027 ingredients for virtual screening. Five compounds with relatively higher docking scores and better absorption, distribution, metabolism, elimination and toxicity (ADMET) parameters were then selected for higher precision docking. The results demonstrated that the potentially active molecules form hydrogen bond interactions with the hinge region residues Met477, Glu475, glycine-rich P-loop residue Val416, Lys430 and DFG motif Asp539. In particular, they also interact with the key residues Thr474 and Cys481 of BTK. The molecular dynamics (MD) results demonstrated that all five compounds above could bind with BTK stably as its cognate ligand in dynamic conditions. This work identified several potential BTKIs using a computer-aided drug design approach and may provide crucial information for developing novel BTKIs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Lili Sun
- Department of Pharmacy, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Zixiao Wang
- Department of Pharmacy, Honghui Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Zhigang Yang
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - XiuJuan Liu
- School of Pharmaceutical Sciences, Institute of Drug Discovery & Development, Key Laboratory of Advanced Drug Preparation Technologies (Ministry of Education), Zhengzhou University, Zhengzhou, China
| | - Haiyan Dong
- Department of Pharmacy, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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Borges EL, Goulart HA, Perin G, Schneider PH, Rieder GS, Nogara PA, da Rocha JBT. One-Pot Synthesis and in Silico Molecular Docking Studies of Arylselanyl Hydrazides as Potential Antituberculosis Agents. Chem Biodivers 2022; 19:e202100793. [PMID: 35293125 DOI: 10.1002/cbdv.202100793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 03/14/2022] [Indexed: 11/06/2022]
Abstract
The present study reports a simple two-step method for the synthesis of arylselanyl hydrazide derivatives using hypophosphorous acid and polyethylene glycol (H3 PO2 /PEG-400) as an alternative reducing system and hydrazine hydrate (NH2 NH2 ⋅xH2 O/50-60 %). This single-vessel procedure was employed with methyl acrylate 2a and methyl bromoacetate 2b using diaryl diselenides to generate the nucleophile species to produce, respectively, 3-(arylselanyl)propane-hydrazides 4a-e and 2-(arylselanyl)acetohydrazides 5a-e with good yields by accelerating the reduction of -Se-Se- bond, when compared to available methods. The synthesized molecules are structurally similar to the isoniazid (INH). Therefore, we perform in silico molecular docking studies, using the lactoperoxidase enzyme, in order to verify whether the INH Se derivatives could interact in a similar way to INH at the active site of the mammalian enzyme. The in silico results indicated a similar type of interaction of the arylselanyl hydrazide derivatives with that of INH. In view of the similar in silico interaction of the selenium derivatives of INH, the arylselanyl hydrazide derivatives reported here should be tested against Mycobacterium tuberculosis in vitro.
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Affiliation(s)
- Elton L Borges
- Grupo de Pesquisa em Síntese Orgânica da Região Amazônica (LASORA, DAEPA), Fundação Universidade Federal de Rondônia (UNIR), Rua da Paz 4376, 76916-000, Presidente Médici, RO, Brazil
| | - Helen A Goulart
- Laboratório de Síntese Orgânica Limpa (LASOL, CCQFA), Universidade Federal de Pelotas (UFPel), PO Box 354, 96010-900, Pelotas, RS, Brazil
| | - Gelson Perin
- Laboratório de Síntese Orgânica Limpa (LASOL, CCQFA), Universidade Federal de Pelotas (UFPel), PO Box 354, 96010-900, Pelotas, RS, Brazil
| | - Paulo H Schneider
- Instituto de Química, Universidade Federal do Rio Grande do Sul (UFRGS), 91501-970, Porto Alegre, RS, Brazil
| | - Guilherme S Rieder
- Programa de Pós-graduação em Ciências Biológicas: Bioquímica Toxicológica, Universidade Federal de Santa Maria (UFSM), 97105-90, Santa Maria, RS, Brazil
| | - Pablo A Nogara
- Programa de Pós-graduação em Ciências Biológicas: Bioquímica Toxicológica, Universidade Federal de Santa Maria (UFSM), 97105-90, Santa Maria, RS, Brazil
| | - João B T da Rocha
- Programa de Pós-graduação em Ciências Biológicas: Bioquímica Toxicológica, Universidade Federal de Santa Maria (UFSM), 97105-90, Santa Maria, RS, Brazil
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Ray R, Shenoy GG, Kumar TNVG. A Comparative Study of 1D Descriptors Supported CoMFA and CoMSIA QSAR Models to Gain Novel Insights into 1,2,4-Triazoles Acting As Antitubercular Agents. Curr Comput Aided Drug Des 2021; 17:281-293. [PMID: 32116196 DOI: 10.2174/1573409916666200302115432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 12/25/2019] [Accepted: 02/14/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Tuberculosis is one of the leading causes of deaths due to infectious disease worldwide. There is an urgent need for developing new drugs due to the rising incidents of drug resistance. Previously, triazole molecules showing antitubercular activity, were reported. Various computational tools pave the way for a rational approach to understanding the structural importance of these compounds in inhibiting the growth of Mycobacterium Tuberculosis. OBJECTIVE The aim of this study is to develop and compare two different QSAR models based on a set of previously reported triazole molecules and use the best one for gaining structural insights into those molecules. METHODS In this current study, two separate models were made with CoMFA and CoMSIA descriptors based on a dataset of triazole molecules showing antitubercular activity. Several one dimensional (1D) descriptors were added to each of the models and the validation results and contour data generated from them were compared. The best model was analysed to give a detailed understanding of the triazole molecules and their role in the antitubercular activity. RESULTS The r2, q2, predicted r2 and SEP (Standard error of prediction) for the CoMFA model were 0.866, 0.573, 0.119 and 0.736 respectively and for the CoMSIA model, the r2, q2, predicted r2 and SEP were calculated to be 0.998, 0.634, 0.013 and 0.869 respectively. Although both the QSAR models produced acceptable internal and external validation scores, but the CoMSIA results were significantly better. The CoMSIA contours also provided a better match than CoMFA with most of the features of the active compound 30b. Hence, the CoMSIA model was chosen and its contours were explored for gaining structural insights into the triazole molecules. CONCLUSION The CoMSIA contours helped us understand the role of several atoms and groups of the triazole molecules in their biological activity. The possibilities for substitution in the triazole compounds that would enhance the activity were also analyzed. Thus, this study paves the way for designing new antitubercular drugs in future.
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Affiliation(s)
- Rajdeep Ray
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Gautham G Shenoy
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - T N V Ganesh Kumar
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
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de Ávila MB, Bitencourt-Ferreira G, de Azevedo WF. Structural Basis for Inhibition of Enoyl-[Acyl Carrier Protein] Reductase (InhA) from Mycobacterium tuberculosis. Curr Med Chem 2020; 27:745-759. [DOI: 10.2174/0929867326666181203125229] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 07/26/2018] [Accepted: 11/14/2018] [Indexed: 12/18/2022]
Abstract
Background::
The enzyme trans-enoyl-[acyl carrier protein] reductase (InhA) is a central
protein for the development of antitubercular drugs. This enzyme is the target for the pro-drug
isoniazid, which is catalyzed by the enzyme catalase-peroxidase (KatG) to become active.
Objective::
Our goal here is to review the studies on InhA, starting with general aspects and focusing on
the recent structural studies, with emphasis on the crystallographic structures of complexes involving
InhA and inhibitors.
Method::
We start with a literature review, and then we describe recent studies on InhA crystallographic
structures. We use this structural information to depict protein-ligand interactions. We also analyze the
structural basis for inhibition of InhA. Furthermore, we describe the application of computational
methods to predict binding affinity based on the crystallographic position of the ligands.
Results::
Analysis of the structures in complex with inhibitors revealed the critical residues responsible
for the specificity against InhA. Most of the intermolecular interactions involve the hydrophobic residues
with two exceptions, the residues Ser 94 and Tyr 158. Examination of the interactions has shown
that many of the key residues for inhibitor binding were found in mutations of the InhA gene in the
isoniazid-resistant Mycobacterium tuberculosis. Computational prediction of the binding affinity for
InhA has indicated a moderate uphill relationship with experimental values.
Conclusion::
Analysis of the structures involving InhA inhibitors shows that small modifications on
these molecules could modulate their inhibition, which may be used to design novel antitubercular
drugs specific for multidrug-resistant strains.
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Affiliation(s)
- Maurício Boff de Ávila
- Laboratory of Computational Systems Biology, School of Sciences - Pontifical Catholic University of Rio, Grande do Sul (PUCRS), Av. Ipiranga, 6681, Porto Alegre-RS 90619-900, Brazil
| | - Gabriela Bitencourt-Ferreira
- Laboratory of Computational Systems Biology, School of Sciences - Pontifical Catholic University of Rio, Grande do Sul (PUCRS), Av. Ipiranga, 6681, Porto Alegre-RS 90619-900, Brazil
| | - Walter Filgueira de Azevedo
- Laboratory of Computational Systems Biology, School of Sciences - Pontifical Catholic University of Rio, Grande do Sul (PUCRS), Av. Ipiranga, 6681, Porto Alegre-RS 90619-900, Brazil
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Perryman AL, Yu W, Wang X, Ekins S, Forli S, Li SG, Freundlich JS, Tonge PJ, Olson AJ. A virtual screen discovers novel, fragment-sized inhibitors of Mycobacterium tuberculosis InhA. J Chem Inf Model 2015; 55:645-59. [PMID: 25636146 DOI: 10.1021/ci500672v] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Isoniazid (INH) is usually administered to treat latent Mycobacterium tuberculosis (Mtb) infections and is used in combination therapy to treat active tuberculosis (TB). Unfortunately, resistance to this drug is hampering its clinical effectiveness. INH is a prodrug that must be activated by Mtb catalase-peroxidase (KatG) before it can inhibit InhA (Mtb enoyl-acyl-carrier-protein reductase). Isoniazid-resistant cases of TB found in clinical settings usually involve mutations in or deletion of katG, which abrogate INH activation. Compounds that inhibit InhA without requiring prior activation by KatG would not be affected by this resistance mechanism and hence would display continued potency against these drug-resistant isolates of Mtb. Virtual screening experiments versus InhA in the GO Fight Against Malaria (GO FAM) project were designed to discover new scaffolds that display base-stacking interactions with the NAD cofactor. GO FAM experiments included targets from other pathogens, including Mtb, when they had structural similarity to a malaria target. Eight of the 16 soluble compounds identified by docking against InhA plus visual inspection were modest inhibitors and did not require prior activation by KatG. The best two inhibitors discovered are both fragment-sized compounds and displayed Ki values of 54 and 59 μM, respectively. Importantly, the novel inhibitors discovered have low structural similarity to known InhA inhibitors and thus help expand the number of chemotypes on which future medicinal chemistry efforts can be focused. These new fragment hits could eventually help advance the fight against INH-resistant Mtb strains, which pose a significant global health threat.
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Affiliation(s)
- Alexander L Perryman
- †Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | | | | | - Sean Ekins
- ⊥Collaborations in Chemistry, 5616 Hilltop Needmore Road, Fuquay-Varina, North Carolina 27526, United States.,#Collaborative Drug Discovery, 1633 Bayshore Highway, Suite 342, Burlingame, California 94010, United States
| | - Stefano Forli
- †Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | | | | | | | - Arthur J Olson
- †Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
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Elucidating the structural basis of diphenyl ether derivatives as highly potent enoyl-ACP reductase inhibitors through molecular dynamics simulations and 3D-QSAR study. J Mol Model 2014; 20:2319. [PMID: 24935113 DOI: 10.1007/s00894-014-2319-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 05/26/2014] [Indexed: 10/25/2022]
Abstract
Diphenyl ether derivatives are good candidates for anti-tuberculosis agents that display a promising potency for inhibition of InhA, an essential enoyl-acyl carrier protein (ACP) reductase involved in fatty acid biosynthesis pathways in Mycobacterium tuberculosis. In this work, key structural features for the inhibition were identified by 3D-QSAR CoMSIA models, constructed based on available experimental binding properties of diphenyl ether inhibitors, and a set of four representative compounds was subjected to MD simulations of inhibitor-InhA complexes for the calculation of binding free energies. The results show that bulky groups are required for the R1 substituent on the phenyl A ring of the inhibitors to favor a hydrophobic pocket formed by residues Phe149, Met155, Pro156, Ala157, Tyr158, Pro193, Met199, Val203, Leu207, Ile215, and Leu218. Small substituents with a hydrophilic property are required at the R3 and R4 positions of the inhibitor phenyl B rings to form hydrogen bonds with the backbones of Gly96 and Met98, respectively. For the R2 substituent, small substituents with simultaneous hydrophilic or hydrophobic properties are required to favor the interaction with the pyrophosphate moiety of NAD(+) and the methyl side chain of Ala198, respectively. The reported data provide structural guidance for the design of new and potent diphenyl ether-based inhibitors with high inhibitory activities against M. tuberculosis InhA.
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Alaoui MAE, Ibrahimi A, Semlali O, Tarhda Z, Marouane M, Najwa A, Soulaymani A, Fahime EE. Affinity comparison of different THCA synthase to CBGA using modeling computational approaches. Bioinformation 2014; 10:33-8. [PMID: 24516324 PMCID: PMC3916817 DOI: 10.6026/97320630010033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Revised: 12/24/2013] [Accepted: 01/06/2014] [Indexed: 11/23/2022] Open
Abstract
The Δ9-Tetrahydrocannabinol (THCA) is the primary psychoactive compound of Cannabis Sativa. It is produced by Δ1-
Tetrahydrocannabinolic acid synthase (THCA) which catalyzes the oxidative cyclization of cannabigerolic acid (CBGA) the
precursor of the THCA. In this study, we were interested by the three dimensional structure of THCA synthase protein. Generation
of models were done by MODELLER v9.11 and homology modeling with Δ1-tetrahydrocannabinolic acid (THCA) synthase X ray
structure (PDB code 3VTE) on the basis of sequences retrieved from GenBank. Procheck, Errat, and Verify 3D tools were used to
verify the reliability of the six 3D models obtained, the overall quality factor and the Prosa Z-score were also used to check the
quality of the six modeled proteins. The RMSDs for C-alpha atoms, main-chain atoms, side-chain atoms and all atoms between the
modeled structures and the corresponding template ranged between 0.290 Å-1.252 Å, reflecting the good quality of the obtained
models. Our study of the CBGA-THCA synthase docking demonstrated that the active site pocket was successfully recognized
using computational approach. The interaction energy of CBGA computed in ‘fiber types’ proteins ranged between -4.1 95
kcal/mol and -5.95 kcal/mol whereas in the ‘drug type’ was about -7.02 kcal/mol to -7.16 kcal/mol, which maybe indicate the
important role played by the interaction energy of CBGA in the determination of the THCA level in Cannabis Sativa L. varieties.
Finally, we have proposed an experimental design in order to explore the binding energy source of ligand-enzyme in Cannabis
Sativa and the production level of the THCA in the absence of any information regarding the correlation between the enzyme
affinity and THCA level production. This report opens the doors to more studies predicting the binding site pocket with accuracy
from the perspective of the protein affinity and THCA level produced in Cannabis Sativa.
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Affiliation(s)
- Moulay Abdelaziz El Alaoui
- Functional Genomic Platform, UATRS, Center for Scientific and Technical Research [CNRST], Rabat, Morocco ; Laboratory of Genetics and Biometry, Faculty of Sciences, University Ibn Tofail
| | - Azeddine Ibrahimi
- MedBiotech Lab, Faculté de Médecine et de Pharmacie de Rabat, Université Mohammed V Souissi
| | - Oussama Semlali
- MedBiotech Lab, Faculté de Médecine et de Pharmacie de Rabat, Université Mohammed V Souissi
| | - Zineb Tarhda
- MedBiotech Lab, Faculté de Médecine et de Pharmacie de Rabat, Université Mohammed V Souissi
| | - Melloul Marouane
- Functional Genomic Platform, UATRS, Center for Scientific and Technical Research [CNRST], Rabat, Morocco ; Laboratory of Genetics and Biometry, Faculty of Sciences, University Ibn Tofail
| | - Alaoui Najwa
- MedBiotech Lab, Faculté de Médecine et de Pharmacie de Rabat, Université Mohammed V Souissi
| | | | - Elmostafa El Fahime
- Functional Genomic Platform, UATRS, Center for Scientific and Technical Research [CNRST], Rabat, Morocco
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da Silva Ribeiro TC, da Costa RF, Bezerra EM, Freire VN, Lyra ML, Manzoni V. The quantum biophysics of the isoniazid adduct NADH binding to its InhA reductase target. NEW J CHEM 2014. [DOI: 10.1039/c3nj01453c] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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