1
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Novak J, Pathak P, Grishina MA, Potemkin VA. The design of compounds with desirable properties - The anti-HIV case study. J Comput Chem 2023; 44:1016-1030. [PMID: 36533526 DOI: 10.1002/jcc.27061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 11/14/2022] [Accepted: 12/04/2022] [Indexed: 12/23/2022]
Abstract
Efficacy and safety are among the most desirable characteristics of an ideal drug. The tremendous increase in computing power and the entry of artificial intelligence into the field of computational drug design are accelerating the process of identifying, developing, and optimizing potential drugs. Here, we present novel approach to design new molecules with desired properties. We combined various neural networks and linear regression algorithms to build models for cytotoxicity and anti-HIV activity based on Continual Molecular Interior analysis (CoMIn) and Cinderella's Shoe (CiS) derived molecular descriptors. After validating the reliability of the models, a genetic algorithm was coupled with the Des-Pot Grid algorithm to generate new molecules from a predefined pool of molecular fragments and predict their bioactivity and cytotoxicity. This combination led to the proposal of 16 hit molecules with high anti-HIV activity and low cytotoxicity. The anti-SARS-CoV-2 activity of the hits was predicted.
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Affiliation(s)
- Jurica Novak
- Department of Biotechnology, University of Rijeka, Rijeka, Croatia
- Center for Artificial Intelligence and Cybersecurity, University of Rijeka, Rijeka, Croatia
- Scientific and Educational Center "Biomedical Technologies", Higher Medical & Biological School, South Ural State University, Chelyabinsk, Russia
| | - Prateek Pathak
- Laboratory of Computational Modelling of Drugs, Higher Medical & Biological School, South Ural State University, Chelyabinsk, Russia
| | - Maria A Grishina
- Laboratory of Computational Modelling of Drugs, Higher Medical & Biological School, South Ural State University, Chelyabinsk, Russia
| | - Vladimir A Potemkin
- Laboratory of Computational Modelling of Drugs, Higher Medical & Biological School, South Ural State University, Chelyabinsk, Russia
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2
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Singh G, Saini A, Mohit, Pawan, Diksha, Sushma, Suman, Priyanka, Satija P. Elucidating the sensing properties of thiophene amended organosilane for detection of chromium(III) ion and its potential activity against HIV-1 RT via computational approach. INORG CHEM COMMUN 2022. [DOI: 10.1016/j.inoche.2022.110090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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3
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Synthesis, biological evaluation, and bioinformatics analysis of indole analogs on AChE and GST activities. Med Chem Res 2022. [DOI: 10.1007/s00044-022-02974-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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4
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Saikia S, Bordoloi M. Molecular Docking: Challenges, Advances and its Use in Drug Discovery Perspective. Curr Drug Targets 2020; 20:501-521. [PMID: 30360733 DOI: 10.2174/1389450119666181022153016] [Citation(s) in RCA: 203] [Impact Index Per Article: 50.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 06/08/2018] [Accepted: 08/28/2018] [Indexed: 01/21/2023]
Abstract
Molecular docking is a process through which small molecules are docked into the macromolecular structures for scoring its complementary values at the binding sites. It is a vibrant research area with dynamic utility in structure-based drug-designing, lead optimization, biochemical pathway and for drug designing being the most attractive tools. Two pillars for a successful docking experiment are correct pose and affinity prediction. Each program has its own advantages and drawbacks with respect to their docking accuracy, ranking accuracy and time consumption so a general conclusion cannot be drawn. Moreover, users don't always consider sufficient diversity in their test sets which results in certain programs to outperform others. In this review, the prime focus has been laid on the challenges of docking and troubleshooters in existing programs, underlying algorithmic background of docking, preferences regarding the use of docking programs for best results illustrated with examples, comparison of performance for existing tools and algorithms, state of art in docking, recent trends of diseases and current drug industries, evidence from clinical trials and post-marketing surveillance are discussed. These aspects of the molecular drug designing paradigm are quite controversial and challenging and this review would be an asset to the bioinformatics and drug designing communities.
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Affiliation(s)
- Surovi Saikia
- Natural Products Chemistry Group, CSIR North East Institute of Science & Technology, Jorhat-785006, Assam, India
| | - Manobjyoti Bordoloi
- Natural Products Chemistry Group, CSIR North East Institute of Science & Technology, Jorhat-785006, Assam, India
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5
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Thiyagarajamoorthy DK, Arulanandam CD, Dahms HU, Murugaiah SG, Krishnan M, Rathinam AJ. Marine Bacterial Compounds Evaluated by In Silico Studies as Antipsychotic Drugs Against Schizophrenia. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2018; 20:639-653. [PMID: 30019186 DOI: 10.1007/s10126-018-9835-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 05/24/2018] [Indexed: 06/08/2023]
Abstract
Schizophrenia (SCZ) is one of the brain disorders which affects the thinking and behavioral skills of patients. This disorder comes along with an overproduction of kynurenic acid in the cerebrospinal fluid and the prefrontal cortex of SCZ patients. In this study, marine bacterial compounds were screened for their suitability as antagonists against human kynurenine aminotransferase (hKAT-1) which causes the synthesis of kynurenic acid downstream which ultimately causes the SCZ disorder according to the kynurenic hypothesis of SCZ. The marine actinobacterial compound bonactin shows more promising results than other tested marine compounds such as the histamine H2 blocker famotidine and indole-3-acetic acid (IAC) from docking and in silico toxicological studies carried out here. The obtained results of the Grid-based Ligand Docking with Energetics (Glide) scores of extra-precision (XP) Glide against the target protein hKAT-1 on IAC, famotidine, and bonactin were - 6.581, - 6.500 and - 7.730 kcal/mol where Glide energies were - 29.84, - 28.391, and - 47.565 kcal/mol, respectively. Bonactin is known as an antibacterial and antifungal compound being extracted from a marine Streptomyces sp. Comparing tested compounds against the drug target hKAT-1, bonactin alone showed the best Glide score and Glide energy on the target protein hKAT-1.
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Affiliation(s)
| | - Charli Deepak Arulanandam
- Department of Biomedical Science and Environmental Biology, KMU- Kaohsiung Medical University, Kaohsiung, 80708, Taiwan, Republic Of China
- Department of Medicinal and Applied Chemistry, KMU- Kaohsiung Medical University, Kaohsiung, 80708, Taiwan, Republic Of China
| | - Hans-Uwe Dahms
- Department of Biomedical Science and Environmental Biology, KMU- Kaohsiung Medical University, Kaohsiung, 80708, Taiwan, Republic Of China.
- Research Center for Environmental Medicine, KMU- Kaohsiung Medical University, Kaohsiung, 80708, Taiwan, Republic Of China.
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan, Republic Of China.
| | - Santhosh Gokul Murugaiah
- Department of Marine Science, Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620 024, India
| | - Muthukumar Krishnan
- Department of Marine Science, Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620 024, India
| | - Arthur James Rathinam
- Department of Marine Science, Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620 024, India.
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6
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Tarasova O, Poroikov V, Veselovsky A. Molecular Docking Studies of HIV-1 Resistance to Reverse Transcriptase Inhibitors: Mini-Review. Molecules 2018; 23:molecules23051233. [PMID: 29883406 PMCID: PMC6100360 DOI: 10.3390/molecules23051233] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 05/15/2018] [Accepted: 05/15/2018] [Indexed: 02/05/2023] Open
Abstract
Currently, millions of people are living with human immunodeficiency virus type 1 (HIV-1), which causes acquired immunodeficiency syndrome. However, the spread of the HIV-1 resistance to antiviral agents is the major problem in the antiretroviral therapy and medical management of HIV-infected patients. HIV-1 reverse transcriptase (RT) is one of the key viral targets for HIV-1 inhibition. Therefore, the studies on the combatting the HIV resistance that occurs due to the structural changes in RT, are in great demand. This work aims to provide an overview of the state-of-the-art molecular docking approaches applied to the studies of the HIV-1 resistance, associated with RT structure changes. We have reviewed recent studies using molecular docking with mutant forms of RT. The work discusses the modifications of molecular docking, which have been developed to find the novel molecules active against resistance mutants of RT and/or recombinant strains of HIV-1. The perspectives of the existing algorithms of molecular docking to the studies on molecular mechanisms of resistance and selection of the correct binding poses for the reverse transcriptase inhibitors are discussed.
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Affiliation(s)
- Olga Tarasova
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya st., Moscow 119121, Russia.
| | - Vladimir Poroikov
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya st., Moscow 119121, Russia.
| | - Alexander Veselovsky
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya st., Moscow 119121, Russia.
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7
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Karimian Amroabadi M, Taheri-Kafrani A, Heidarpoor Saremi L, Rastegari AA. Spectroscopic studies of the interaction between alprazolam and apo-human serum transferrin as a drug carrier protein. Int J Biol Macromol 2018; 108:263-271. [DOI: 10.1016/j.ijbiomac.2017.11.179] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 11/29/2017] [Accepted: 11/30/2017] [Indexed: 01/20/2023]
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8
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Kong X, Sun H, Pan P, Zhu F, Chang S, Xu L, Li Y, Hou T. Importance of protein flexibility in molecular recognition: a case study on Type-I1/2 inhibitors of ALK. Phys Chem Chem Phys 2018; 20:4851-4863. [DOI: 10.1039/c7cp08241j] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Anaplastic lymphoma kinase (ALK) has been regarded as a promising target for the therapy of various cancers.
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Affiliation(s)
- Xiaotian Kong
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- P. R. China
- Institute of Functional Nano and Soft Materials (FUNSOM)
| | - Huiyong Sun
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- P. R. China
| | - Peichen Pan
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- P. R. China
| | - Feng Zhu
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- P. R. China
| | - Shan Chang
- Institute of Bioinformatics and Medical Engineering
- School of Electrical and Information Engineering
- Jiangsu University of Technology
- Changzhou 213001
- P. R. China
| | - Lei Xu
- Institute of Bioinformatics and Medical Engineering
- School of Electrical and Information Engineering
- Jiangsu University of Technology
- Changzhou 213001
- P. R. China
| | - Youyong Li
- Institute of Functional Nano and Soft Materials (FUNSOM)
- Soochow University
- Suzhou
- P. R. China
| | - Tingjun Hou
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- P. R. China
- Institute of Functional Nano and Soft Materials (FUNSOM)
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9
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Frączek T, Kamiński R, Krakowiak A, Naessens E, Verhasselt B, Paneth P. Diaryl ethers with carboxymethoxyphenacyl motif as potent HIV-1 reverse transcriptase inhibitors with improved solubility. J Enzyme Inhib Med Chem 2017; 33:9-16. [PMID: 29098886 PMCID: PMC6009982 DOI: 10.1080/14756366.2017.1387542] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
In search of new non-nucleoside reverse transcriptase inhibitors (NNRTIs) with improved solubility, two series of novel diaryl ethers with phenacyl moiety were designed and evaluated for their HIV-1 reverse transcriptase inhibition potentials. All compounds exhibited good to excellent results with IC50 at low micromolar to submicromolar concentrations. Two most active compounds (7e and 7 g) exhibit inhibitory potency comparable or even better than that of nevirapine and rilpivirine. Furthermore, SupT1 and CD4+ cell infectivity assays for the most promising (7e) have confirmed its strong antiviral potential while docking studies indicate a novel binding interactions responsible for high activity.
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Affiliation(s)
- Tomasz Frączek
- a Institute of Applied Radiation Chemistry , Lodz University of Technology , Lodz , Poland
| | - Rafał Kamiński
- a Institute of Applied Radiation Chemistry , Lodz University of Technology , Lodz , Poland
| | - Agnieszka Krakowiak
- a Institute of Applied Radiation Chemistry , Lodz University of Technology , Lodz , Poland.,b Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies , Polish Academy of Sciences , Lodz , Poland
| | - Evelien Naessens
- c Department of Clinical Chemistry, Microbiology and Immunology , Ghent University, Ghent University Hospital , Ghent , Belgium
| | - Bruno Verhasselt
- c Department of Clinical Chemistry, Microbiology and Immunology , Ghent University, Ghent University Hospital , Ghent , Belgium
| | - Piotr Paneth
- a Institute of Applied Radiation Chemistry , Lodz University of Technology , Lodz , Poland
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10
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Samanta PN, Das KK. Inhibition activities of catechol diether based non-nucleoside inhibitors against the HIV reverse transcriptase variants: Insights from molecular docking and ONIOM calculations. J Mol Graph Model 2017. [DOI: 10.1016/j.jmgm.2017.06.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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11
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Mtiraoui H, Nsira A, Msaddek M, Renard PY, Sabot C. Regioselective synthesis of o -triazolyl-1,5-benzodiazepin-2-ones and o -isoxazolyl-1,5-benzodiazepin-2-ones via copper-catalyzed 1,3-dipolar cycloaddition reactions. CR CHIM 2017. [DOI: 10.1016/j.crci.2017.02.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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12
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Abstract
Docking, a molecular modelling method, has wide applications in identification and optimization in modern drug discovery. This chapter addresses the recent advances in the docking methodologies like fragment docking, covalent docking, inverse docking, post processing, hybrid techniques, homology modeling etc. and its protocol like searching and scoring functions. Advances in scoring functions for e.g. consensus scoring, quantum mechanics methods, clustering and entropy based methods, fingerprinting, etc. are used to overcome the limitations of the commonly used force-field, empirical and knowledge based scoring functions. It will cover crucial necessities and different algorithms of docking and scoring. Further different aspects like protein flexibility, ligand sampling and flexibility, and the performance of scoring function will be discussed.
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Affiliation(s)
- Ashwani Kumar
- Guru Jambheshwar University of Science and Technology, India
| | - Ruchika Goyal
- Guru Jambheshwar University of Science and Technology, India
| | - Sandeep Jain
- Guru Jambheshwar University of Science and Technology, India
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13
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Santos LH, Ferreira RS, Caffarena ER. Computational drug design strategies applied to the modelling of human immunodeficiency virus-1 reverse transcriptase inhibitors. Mem Inst Oswaldo Cruz 2016; 110:847-64. [PMID: 26560977 PMCID: PMC4660614 DOI: 10.1590/0074-02760150239] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 09/08/2015] [Indexed: 01/05/2023] Open
Abstract
Reverse transcriptase (RT) is a multifunctional enzyme in the human immunodeficiency
virus (HIV)-1 life cycle and represents a primary target for drug discovery efforts
against HIV-1 infection. Two classes of RT inhibitors, the nucleoside RT inhibitors
(NRTIs) and the nonnucleoside transcriptase inhibitors are prominently used in the
highly active antiretroviral therapy in combination with other anti-HIV drugs.
However, the rapid emergence of drug-resistant viral strains has limited the
successful rate of the anti-HIV agents. Computational methods are a significant part
of the drug design process and indispensable to study drug resistance. In this
review, recent advances in computer-aided drug design for the rational design of new
compounds against HIV-1 RT using methods such as molecular docking, molecular
dynamics, free energy calculations, quantitative structure-activity relationships,
pharmacophore modelling and absorption, distribution, metabolism, excretion and
toxicity prediction are discussed. Successful applications of these methodologies are
also highlighted.
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Affiliation(s)
| | - Rafaela Salgado Ferreira
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil
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14
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Tintori C, Brai A, Dasso Lang MC, Deodato D, Greco AM, Bizzarri BM, Cascone L, Casian A, Zamperini C, Dreassi E, Crespan E, Maga G, Vanham G, Ceresola E, Canducci F, Ariën KK, Botta M. Development and in Vitro Evaluation of a Microbicide Gel Formulation for a Novel Non-Nucleoside Reverse Transcriptase Inhibitor Belonging to the N-Dihydroalkyloxybenzyloxopyrimidines (N-DABOs) Family. J Med Chem 2016; 59:2747-59. [PMID: 26898379 DOI: 10.1021/acs.jmedchem.5b01979] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Preventing HIV transmission by the use of a vaginal microbicide is a topic of considerable interest in the fight against AIDS. Both a potent anti-HIV agent and an efficient formulation are required to develop a successful microbicide. In this regard, molecules able to inhibit the HIV replication before the integration of the viral DNA into the genetic material of the host cells, such as entry inhibitors or reverse transcriptase inhibitors (RTIs), are ideal candidates for prevention purpose. Among RTIs, S- and N-dihydroalkyloxybenzyloxopyrimidines (S-DABOs and N-DABOs) are interesting compounds active at nanomolar concentration against wild type of RT and with a very interesting activity against RT mutations. Herein, novel N-DABOs were synthesized and tested as anti-HIV agents. Furthermore, their mode of binding was studied by molecular modeling. At the same time, a vaginal microbicide gel formulation was developed and tested for one of the most promising candidates.
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Affiliation(s)
- Cristina Tintori
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena , Via A. De Gasperi 2, I-53100 Siena, Italy
| | - Annalaura Brai
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena , Via A. De Gasperi 2, I-53100 Siena, Italy
| | - Maria Chiara Dasso Lang
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena , Via A. De Gasperi 2, I-53100 Siena, Italy
| | - Davide Deodato
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena , Via A. De Gasperi 2, I-53100 Siena, Italy
| | - Antonia Michela Greco
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena , Via A. De Gasperi 2, I-53100 Siena, Italy
| | - Bruno Mattia Bizzarri
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena , Via A. De Gasperi 2, I-53100 Siena, Italy
| | - Lorena Cascone
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena , Via A. De Gasperi 2, I-53100 Siena, Italy
| | - Alexandru Casian
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena , Via A. De Gasperi 2, I-53100 Siena, Italy
| | - Claudio Zamperini
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena , Via A. De Gasperi 2, I-53100 Siena, Italy
| | - Elena Dreassi
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena , Via A. De Gasperi 2, I-53100 Siena, Italy
| | - Emmanuele Crespan
- Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Giovanni Maga
- Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Guido Vanham
- Virology Unit, Institute of Tropical Medicine , Nationalestraat 155, B-2000 Antwerpen, Belgium
| | - Elisa Ceresola
- Department of Biotechnology and Life Sciences, University of Insubria , Dunant 3, 21100, Varese, Italy
| | - Filippo Canducci
- Department of Biotechnology and Life Sciences, University of Insubria , Dunant 3, 21100, Varese, Italy
| | - Kevin K Ariën
- Virology Unit, Institute of Tropical Medicine , Nationalestraat 155, B-2000 Antwerpen, Belgium
| | - Maurizio Botta
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena , Via A. De Gasperi 2, I-53100 Siena, Italy.,Biotechnology College of Science and Technology, Temple University , Biolife Science Building, Suite 333, 1900 N 12th Street, Philadelphia, Pennsylvania 19122, United States
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15
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Lin CP, Boysen RI, Campi EM, Saito K, Hearn MTW. Studies on the binding sites of IgG2 monoclonal antibodies recognized by terpyridine-based affinity ligands. J Mol Recognit 2016; 29:334-42. [PMID: 26842829 DOI: 10.1002/jmr.2535] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 12/16/2015] [Indexed: 11/09/2022]
Abstract
This investigation has examined the origin of the molecular recognition associated with the interaction of monoclonal IgG2's with terpyridine-based ligands immobilized onto agarose-derived chromatographic adsorbents. Isothermal titration calorimetric (ITC) methods have been employed to acquire thermodynamic data associated with the IgG2-ligand binding. These ITC investigations have documented that different enthalpic and entropic processes are involved depending on the nature of the chemical substituents in the core structure of the terpyridinyl moiety. In addition, molecular docking studies have been carried out with IgG2 structures with the objective to identify possible ligand binding sites and key interacting amino acid residues. These molecular docking experiments with the different terpyridine-based ligands have shown that all of the examined ligands can potentially undergo favorable interactions with a site located within the Fab region of the IgG2. However, another favorable binding site was also identified from the docking poses to exist within the Fc region of the IgG2 for some, but not all, of the ligands studied. These investigations have provided a basis to elucidate the unique binding properties and chromatographic behaviors shown by several substituted terpyridine ligands in their interaction with IgGs of different isotype. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Chih-Pei Lin
- School of Chemistry, Monash University, Melbourne, VIC, 3800, Australia
| | - Reinhard I Boysen
- School of Chemistry, Monash University, Melbourne, VIC, 3800, Australia
| | - Eva M Campi
- School of Chemistry, Monash University, Melbourne, VIC, 3800, Australia
| | - Kei Saito
- School of Chemistry, Monash University, Melbourne, VIC, 3800, Australia
| | - Milton T W Hearn
- School of Chemistry, Monash University, Melbourne, VIC, 3800, Australia
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16
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Choi J, Choi KE, Park SJ, Kim SY, Jee JG. Ensemble-Based Virtual Screening Led to the Discovery of New Classes of Potent Tyrosinase Inhibitors. J Chem Inf Model 2016; 56:354-67. [DOI: 10.1021/acs.jcim.5b00484] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Joonhyeok Choi
- Research
Institute of Pharmaceutical Sciences, College of Pharmacy, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 702-701, Republic of Korea
| | - Kwang-Eun Choi
- Research
Institute of Pharmaceutical Sciences, College of Pharmacy, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 702-701, Republic of Korea
| | - Sung Jean Park
- College
of Pharmacy, Gachon University, Incheon 406-799, Republic of Korea
| | - Sun Yeou Kim
- College
of Pharmacy, Gachon University, Incheon 406-799, Republic of Korea
| | - Jun-Goo Jee
- Research
Institute of Pharmaceutical Sciences, College of Pharmacy, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 702-701, Republic of Korea
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17
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Chaput L, Martinez-Sanz J, Quiniou E, Rigolet P, Saettel N, Mouawad L. vSDC: a method to improve early recognition in virtual screening when limited experimental resources are available. J Cheminform 2016; 8:1. [PMID: 26807156 PMCID: PMC4722699 DOI: 10.1186/s13321-016-0112-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 01/08/2016] [Indexed: 01/10/2023] Open
Abstract
Background In drug design, one may be confronted to the problem of finding hits for targets for which no small inhibiting molecules are known and only low-throughput experiments are available (like ITC or NMR studies), two common difficulties encountered in a typical academic setting. Using a virtual screening strategy like docking can alleviate some of the problems and save a considerable amount of time by selecting only top-ranking molecules, but only if the method is very efficient, i.e. when a good proportion of actives are found in the 1–10 % best ranked molecules. Results The use of several programs (in our study, Gold, Surflex, FlexX and Glide were considered) shows a divergence of the results, which presents a difficulty in guiding the experiments. To overcome this divergence and increase the yield of the virtual screening, we created the standard deviation consensus (SDC) and variable SDC (vSDC) methods, consisting of the intersection of molecule sets from several virtual screening programs, based on the standard deviations of their ranking distributions. Conclusions SDC allowed us to find hits for two new protein targets by testing only 9 and 11 small molecules from a chemical library of circa 15,000 compounds. Furthermore, vSDC, when applied to the 102 proteins of the DUD-E benchmarking database, succeeded in finding more hits than any of the four isolated programs for 13–60 % of the targets. In addition, when only 10 molecules of each of the 102 chemical libraries were considered, vSDC performed better in the number of hits found, with an improvement of 6–24 % over the 10 best-ranked molecules given by the individual docking programs.In drug design, for a given target and a given chemical library, the results obtained with different virtual screening programs are divergent. So how to rationally guide the experimental tests, especially when only a few number of experiments can be made? The variable Standard Deviation Consensus (vSDC) method was developed to answer this issue. Left panel the vSDC principle consists of intersecting molecule sets, chosen on the basis of the standard deviations of their ranking distributions, obtained from various virtual screening programs. In this study Glide, Gold, FlexX and Surflex were used and tested on the 102 targets of the DUD-E database. Right panel Comparison of the average percentage of hits found with vSDC and each of the four programs, when only 10 molecules from each of the 102 chemical libraries of the DUD-E database were considered. On average, vSDC was capable of finding 38 % of the findable hits, against 34 % for Glide, 32 % for Gold, 16 % for FlexX and 14 % for Surflex, showing that with vSDC, it was possible to overcome the unpredictability of the virtual screening results and to improve them ![]() Electronic supplementary material The online version of this article (doi:10.1186/s13321-016-0112-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ludovic Chaput
- Chemistry, Modelling and Imaging for Biology (CMIB), Centre de Recherche, Institut Curie-PSL Research University, Bâtiment 112, Centre Universitaire, 91405 Orsay Cedex, France ; Paris-Sud University, Orsay, France ; Inserm, U1196, Orsay, France ; CNRS, UMR 9187, Orsay, France
| | - Juan Martinez-Sanz
- Chemistry, Modelling and Imaging for Biology (CMIB), Centre de Recherche, Institut Curie-PSL Research University, Bâtiment 112, Centre Universitaire, 91405 Orsay Cedex, France ; Paris-Sud University, Orsay, France ; Inserm, U1196, Orsay, France ; CNRS, UMR 9187, Orsay, France
| | - Eric Quiniou
- Chemistry, Modelling and Imaging for Biology (CMIB), Centre de Recherche, Institut Curie-PSL Research University, Bâtiment 112, Centre Universitaire, 91405 Orsay Cedex, France ; Paris-Sud University, Orsay, France ; Inserm, U1196, Orsay, France ; CNRS, UMR 9187, Orsay, France
| | - Pascal Rigolet
- Chemistry, Modelling and Imaging for Biology (CMIB), Centre de Recherche, Institut Curie-PSL Research University, Bâtiment 112, Centre Universitaire, 91405 Orsay Cedex, France ; Paris-Sud University, Orsay, France ; Inserm, U1196, Orsay, France ; CNRS, UMR 9187, Orsay, France
| | - Nicolas Saettel
- Chemistry, Modelling and Imaging for Biology (CMIB), Centre de Recherche, Institut Curie-PSL Research University, Bâtiment 112, Centre Universitaire, 91405 Orsay Cedex, France ; Inserm, U1196, Orsay, France ; CNRS, UMR 9187, Orsay, France ; School of Pharmacy, University of Caen, Normandy, Boulevard Becquerel, Caen, 14032 France
| | - Liliane Mouawad
- Chemistry, Modelling and Imaging for Biology (CMIB), Centre de Recherche, Institut Curie-PSL Research University, Bâtiment 112, Centre Universitaire, 91405 Orsay Cedex, France ; Paris-Sud University, Orsay, France ; Inserm, U1196, Orsay, France ; CNRS, UMR 9187, Orsay, France
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Krzemińska A, Świderek KP, Paneth P. Theoretical studies of energetics and binding isotope effects of binding a triazole-based inhibitor to HIV-1 reverse transcriptase. Phys Chem Chem Phys 2016; 18:310-7. [DOI: 10.1039/c5cp06050h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The 18O binding isotope effect allows us to distinguish the actual binding site of an inhibitor in HIV-1 reverse transcriptase.
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Affiliation(s)
- A. Krzemińska
- Institute of Applied Radiation Chemistry
- Lodz University of Technology
- 90-924 Lodz
- Poland
| | - K. P. Świderek
- Institute of Applied Radiation Chemistry
- Lodz University of Technology
- 90-924 Lodz
- Poland
- Department de Quimica Fisica i Analitica
| | - P. Paneth
- Institute of Applied Radiation Chemistry
- Lodz University of Technology
- 90-924 Lodz
- Poland
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19
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Bonsaii M, Gholivand K, Abdi K, Valmoozi AAE, Khosravi M. A combined experimental and computational study on the interaction of nitrogen mustards with DNA. MEDCHEMCOMM 2016. [DOI: 10.1039/c6md00264a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In the present work, we suggest that the role of water in the reaction of nitrogen mustards with DNA is more than what was thought before. Nitrogen mustards become activated when they are hydrated by water.
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Affiliation(s)
- Mahyar Bonsaii
- Department of Chemistry
- Islamic Azad University
- Tehran
- Iran
| | | | - Khosrou Abdi
- Department of Medicinal Chemistry and Radiopharmacy
- Tehran University of Medical Sciences
- Tehran
- Iran
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20
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Li W, Li X, De Clercq E, Zhan P, Liu X. Discovery of potent HIV-1 non-nucleoside reverse transcriptase inhibitors from arylthioacetanilide structural motif. Eur J Med Chem 2015; 102:167-79. [DOI: 10.1016/j.ejmech.2015.07.043] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 07/20/2015] [Accepted: 07/22/2015] [Indexed: 11/26/2022]
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21
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Frączek T, Paneth A, Kamiński R, Krakowiak A, Paneth P. Searching for novel scaffold of triazole non-nucleoside inhibitors of HIV-1 reverse transcriptase. J Enzyme Inhib Med Chem 2015; 31:481-9. [PMID: 25942362 DOI: 10.3109/14756366.2015.1039531] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Azoles are a promising class of the new generation of HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTIs). From thousands of reported compounds, many possess the same basic structure of an aryl substituted azole ring linked by a thioglycolamide chain with another aromatic ring. In order to find novel extensions for this basic scaffold, we explored the 5-position substitution pattern of triazole NNRTIs using molecular docking followed by the synthesis of selected compounds. We found that heterocyclic substituents in the 5-position of the triazole ring are detrimental to the inhibitory activity of compounds with four-membered thioglycolamide linker and this substitution seems to be viable only for compounds with shorter two-membered linker. Promising compound, N-(4-carboxy-2-chlorophenyl)-2-((4-benzyl-5-methyl-4H-1,2,4-triazol-3-yl)sulfanyl)acetamide, with potent inhibitory activity and acceptable aqueous solubility has been identified in this study that could serve as lead scaffold for the development of novel water-soluble salts of triazole NNRTIs.
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Affiliation(s)
- Tomasz Frączek
- a Institute of Applied Radiation Chemistry, Lodz University of Technology , Lodz , Poland
| | - Agata Paneth
- a Institute of Applied Radiation Chemistry, Lodz University of Technology , Lodz , Poland .,b Department of Organic Chemistry , Faculty of Pharmacy, Medical University , Lublin , Poland , and
| | - Rafał Kamiński
- a Institute of Applied Radiation Chemistry, Lodz University of Technology , Lodz , Poland
| | - Agnieszka Krakowiak
- a Institute of Applied Radiation Chemistry, Lodz University of Technology , Lodz , Poland .,c Department of Bioorganic Chemistry , Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences , Lodz , Poland
| | - Piotr Paneth
- a Institute of Applied Radiation Chemistry, Lodz University of Technology , Lodz , Poland
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22
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Esmaeeli Nieh S, Madou MRZ, Sirajuddin M, Fregeau B, McKnight D, Lexa K, Strober J, Spaeth C, Hallinan BE, Smaoui N, Pappas JG, Burrow TA, McDonald MT, Latibashvili M, Leshinsky-Silver E, Lev D, Blumkin L, Vale RD, Barkovich AJ, Sherr EH. De novo mutations in KIF1A cause progressive encephalopathy and brain atrophy. Ann Clin Transl Neurol 2015; 2:623-35. [PMID: 26125038 PMCID: PMC4479523 DOI: 10.1002/acn3.198] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 03/04/2015] [Indexed: 12/30/2022] Open
Abstract
Objective To determine the cause and course of a novel syndrome with progressive encephalopathy and brain atrophy in children. Methods Clinical whole-exome sequencing was performed for global developmental delay and intellectual disability; some patients also had spastic paraparesis and evidence of clinical regression. Six patients were identified with de novo missense mutations in the kinesin gene KIF1A. The predicted functional disruption of these mutations was assessed in silico to compare the calculated conformational flexibility and estimated efficiency of ATP binding to kinesin motor domains of wild-type (WT) versus mutant alleles. Additionally, an in vitro microtubule gliding assay was performed to assess the effects of de novo dominant, inherited recessive, and polymorphic variants on KIF1A motor function. Results All six subjects had severe developmental delay, hypotonia, and varying degrees of hyperreflexia and spastic paraparesis. Microcephaly, cortical visual impairment, optic neuropathy, peripheral neuropathy, ataxia, epilepsy, and movement disorders were also observed. All six patients had a degenerative neurologic course with progressive cerebral and cerebellar atrophy seen on sequential magnetic resonance imaging scans. Computational modeling of mutant protein structures when compared to WT kinesin showed substantial differences in conformational flexibility and ATP-binding efficiency. The de novo KIF1A mutants were nonmotile in the microtubule gliding assay. Interpretation De novo mutations in KIF1A cause a degenerative neurologic syndrome with brain atrophy. Computational and in vitro assays differentiate the severity of dominant de novo heterozygous versus inherited recessive KIF1A mutations. The profound effect de novo mutations have on axonal transport is likely related to the cause of progressive neurologic impairment in these patients.
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Affiliation(s)
- Sahar Esmaeeli Nieh
- Department of Neurology, University of California San Francisco, California, 94158
| | - Maura R Z Madou
- Department of Neurology, University of California San Francisco, California, 94158
| | - Minhajuddin Sirajuddin
- Department of Cellular and Molecular Pharmacology and the Howard Hughes Medical Institute, University of California San Francisco, California ; Cardiovascular Biology and Diseases, Institute of Stem Cell Biology and Regenerative Medicine, NCBS-TIFR Bangalore, India
| | - Brieana Fregeau
- Department of Neurology, University of California San Francisco, California, 94158
| | | | - Katrina Lexa
- Department of Pharmaceutical Chemistry, University of California San Francisco San Francisco, California
| | - Jonathan Strober
- Department of Neurology, University of California San Francisco, California, 94158
| | - Christine Spaeth
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center Cincinnati, Ohio
| | - Barbara E Hallinan
- Division of Neurology, Cincinnati Children's Hospital Medical Center Cincinnati, Ohio
| | | | - John G Pappas
- Department of Pediatrics, Clinical Genetic Services, NYU School of Medicine New York, New York
| | - Thomas A Burrow
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center Cincinnati, Ohio ; Department of pediatrics, University of Cincinnati School of Medicine Cincinnati, Ohio
| | - Marie T McDonald
- Section of Medical Genetics, Department of Pediatrics, Duke University Durham, North Carolina
| | - Mariam Latibashvili
- Department of Neurology, University of California San Francisco, California, 94158 ; University of California San Diego, California
| | - Esther Leshinsky-Silver
- Molecular Genetics Laboratory, and Metabolic-Neurogenetic Service, Wolfson Medical Center and Sackler Medical School, Tel Aviv University Tel Aviv, Israel
| | - Dorit Lev
- Institute of Medical Genetics and Metabolic Neurogenetic Service, Wolfson Medical Center and Sackler Medical School, Tel Aviv University Tel Aviv, Israel
| | - Luba Blumkin
- Pediatric Neurology Unit and Metabolic Neurogenetic Service, Wolfson Medical Center, Holon and Sackler Medical School, Tel Aviv University Tel Aviv, Israel
| | - Ronald D Vale
- Department of Cellular and Molecular Pharmacology and the Howard Hughes Medical Institute, University of California San Francisco, California
| | - Anthony James Barkovich
- Department of Radiology and Biomedical Imaging, University of California San Francisco, California
| | - Elliott H Sherr
- Department of Neurology, University of California San Francisco, California, 94158
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23
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Yuriev E, Holien J, Ramsland PA. Improvements, trends, and new ideas in molecular docking: 2012-2013 in review. J Mol Recognit 2015; 28:581-604. [PMID: 25808539 DOI: 10.1002/jmr.2471] [Citation(s) in RCA: 159] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Revised: 01/16/2015] [Accepted: 02/05/2015] [Indexed: 12/11/2022]
Abstract
Molecular docking is a computational method for predicting the placement of ligands in the binding sites of their receptor(s). In this review, we discuss the methodological developments that occurred in the docking field in 2012 and 2013, with a particular focus on the more difficult aspects of this computational discipline. The main challenges and therefore focal points for developments in docking, covered in this review, are receptor flexibility, solvation, scoring, and virtual screening. We specifically deal with such aspects of molecular docking and its applications as selection criteria for constructing receptor ensembles, target dependence of scoring functions, integration of higher-level theory into scoring, implicit and explicit handling of solvation in the binding process, and comparison and evaluation of docking and scoring methods.
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Affiliation(s)
- Elizabeth Yuriev
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia
| | - Jessica Holien
- ACRF Rational Drug Discovery Centre and Structural Biology Laboratory, St. Vincent's Institute of Medical Research, Fitzroy, Victoria, 3065, Australia
| | - Paul A Ramsland
- Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria, 3004, Australia.,Department of Surgery Austin Health, University of Melbourne, Melbourne, Victoria, 3084, Australia.,Department of Immunology, Monash University, Alfred Medical Research and Education Precinct, Melbourne, Victoria, 3004, Australia.,School of Biomedical Sciences, CHIRI Biosciences, Curtin University, Perth, Western Australia, 6845, Australia
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24
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Kong X, Pan P, Li D, Tian S, Li Y, Hou T. Importance of protein flexibility in ranking inhibitor affinities: modeling the binding mechanisms of piperidine carboxamides as Type I1/2 ALK inhibitors. Phys Chem Chem Phys 2015; 17:6098-113. [DOI: 10.1039/c4cp05440g] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Anaplastic lymphoma kinase (ALK) has gained increased attention as an attractive therapeutic target for the treatment of various cancers, especially non-small-cell lung cancer (NSCLC).
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Affiliation(s)
- Xiaotian Kong
- Institute of Functional Nano and Soft Materials (FUNSOM)
- Soochow University
- Suzhou
- China
| | - Peichen Pan
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- China
| | - Dan Li
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- China
| | - Sheng Tian
- Institute of Functional Nano and Soft Materials (FUNSOM)
- Soochow University
- Suzhou
- China
| | - Youyong Li
- Institute of Functional Nano and Soft Materials (FUNSOM)
- Soochow University
- Suzhou
- China
| | - Tingjun Hou
- Institute of Functional Nano and Soft Materials (FUNSOM)
- Soochow University
- Suzhou
- China
- College of Pharmaceutical Sciences
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25
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Gu WG, Zhang X, Yuan JF. Anti-HIV drug development through computational methods. AAPS JOURNAL 2014; 16:674-80. [PMID: 24760437 DOI: 10.1208/s12248-014-9604-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 04/02/2014] [Indexed: 11/30/2022]
Abstract
Although highly active antiretroviral therapy (HAART) is effective in controlling the progression of AIDS, the emergence of drug-resistant strains increases the difficulty of successful treatment of patients with HIV infection. Increasing numbers of patients are facing the dilemma that comes with the running out of drug combinations for HAART. Computational methods play a key role in anti-HIV drug development. A substantial number of studies have been performed in anti-HIV drug development using various computational methods, such as virtual screening, QSAR, molecular docking, and homology modeling, etc. In this review, we summarize recent advances in the application of computational methods to anti-HIV drug development for five key targets as follows: reverse transcriptase, protease, integrase, CCR5, and CXCR4. We hope that this review will stimulate researchers from multiple disciplines to consider computational methods in the anti-HIV drug development process.
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Affiliation(s)
- Wan-Gang Gu
- Department of Immunology, Zunyi Medical University, Zunyi, 563003, Guizhou, China,
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