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Marković V, Szczepańska A, Berlicki Ł. Antiviral Protein-Protein Interaction Inhibitors. J Med Chem 2024; 67:3205-3231. [PMID: 38394369 PMCID: PMC10945500 DOI: 10.1021/acs.jmedchem.3c01543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 01/04/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024]
Abstract
Continually repeating outbreaks of pathogenic viruses necessitate the construction of effective antiviral strategies. Therefore, the development of new specific antiviral drugs in a well-established and efficient manner is crucial. Taking into account the strong ability of viruses to change, therapies with diversified molecular targets must be sought. In addition to the widely explored viral enzyme inhibitor approach, inhibition of protein-protein interactions is a very valuable strategy. In this Perspective, protein-protein interaction inhibitors targeting HIV, SARS-CoV-2, HCV, Ebola, Dengue, and Chikungunya viruses are reviewed and discussed. Antibodies, peptides/peptidomimetics, and small molecules constitute three classes of compounds that have been explored, and each of them has some advantages and disadvantages for drug development.
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Affiliation(s)
- Violeta Marković
- Wrocław
University of Science and Technology, Department
of Bioorganic Chemistry, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland
- University
of Kragujevac, Faculty of Science,
Department of Chemistry, R. Domanovića 12, 34000 Kragujevac, Serbia
| | - Anna Szczepańska
- Wrocław
University of Science and Technology, Department
of Bioorganic Chemistry, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Łukasz Berlicki
- Wrocław
University of Science and Technology, Department
of Bioorganic Chemistry, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland
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2
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Curreli F, Kwon YD, Nicolau I, Burgos G, Altieri A, Kurkin AV, Verardi R, Kwong PD, Debnath AK. Antiviral Activity and Crystal Structures of HIV-1 gp120 Antagonists. Int J Mol Sci 2022; 23:ijms232415999. [PMID: 36555641 PMCID: PMC9784924 DOI: 10.3390/ijms232415999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/10/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
As part of our effort to discover drugs that target HIV-1 entry, we report the antiviral activity and crystal structures of two novel inhibitors in a complex with a gp120 core. NBD-14204 showed similar antiviral activity against all the clinical isolates tested. The IC50 values were in the range of 0.24-0.9 µM with an overall mean of 0.47 ± 0.03 µM, showing slightly better activity against the clinical isolates than against the lab-adapted HIV-1HXB2 (IC50 = 0.96 ± 0.1 µM). Moreover, the antiviral activity of NBD-14208 was less consistent, showing a wider range of IC50 values (0.66-5.7 µM) with an overall mean of 3 ± 0.25 µM and better activity against subtypes B and D (Mean IC50 2.2-2.5 µM) than the A, C and Rec viruses (Mean IC50 2.9-3.9 µM). SI of NBD-14204 was about 10-fold higher than NBD-14208, making it a better lead compound for further optimization. In addition, we tested these compounds against S375Y and S375H mutants of gp120, which occurred in some clades and observed these to be sensitive to NBD-14204 and NBD-14208. These inhibitors also showed modest activity against HIV-1 reverse transcriptase. Furthermore, we determined the crystal structures of both inhibitors in complexes with gp120 cores. As expected, both NBD-14204 and NBD-14208 bind primarily within the Phe43 cavity. It is noteworthy that the electron density of the thiazole ring in both structures was poorly defined due to the flexibility of this scaffold, suggesting that these compounds maintain substantial entropy, even when bound to the Phe43 cavity.
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Affiliation(s)
- Francesca Curreli
- Laboratory of Molecular Modeling and Drug Design, Lindsey F. Kimball Research Institute, New York Blood Center, New York, NY 10065, USA
| | - Young D. Kwon
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Isabella Nicolau
- Laboratory of Molecular Modeling and Drug Design, Lindsey F. Kimball Research Institute, New York Blood Center, New York, NY 10065, USA
| | - Giancarla Burgos
- Laboratory of Molecular Modeling and Drug Design, Lindsey F. Kimball Research Institute, New York Blood Center, New York, NY 10065, USA
| | - Andrea Altieri
- EDASA Scientific srls, Via Stingi 37, 66050 San Salvo, Italy
| | | | - Raffaello Verardi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter D. Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Asim K. Debnath
- Laboratory of Molecular Modeling and Drug Design, Lindsey F. Kimball Research Institute, New York Blood Center, New York, NY 10065, USA
- Correspondence:
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Alshorman A, Al-Hosainat N, Jackson T. Analysis of HIV latent infection model with multiple infection stages and different drug classes. JOURNAL OF BIOLOGICAL DYNAMICS 2022; 16:713-732. [PMID: 36264087 DOI: 10.1080/17513758.2022.2113828] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 08/09/2022] [Indexed: 06/16/2023]
Abstract
Latently infected CD4+ T cells represent one of the major obstacles to HIV eradication even after receiving prolonged highly active anti-retroviral therapy (HAART). Long-term use of HAART causes the emergence of drug-resistant virus which is then involved in HIV transmission. In this paper, we develop mathematical HIV models with staged disease progression by incorporating entry inhibitor and latently infected cells. We find that entry inhibitor has the same effect as protease inhibitor on the model dynamics and therefore would benefit HIV patients who developed resistance to many of current anti-HIV medications. Numerical simulations illustrate the theoretical results and show that the virus and latently infected cells reach an infected steady state in the absence of treatment and are eliminated under treatment whereas the model including homeostatic proliferation of latently infected cells maintains the virus at low level during suppressive treatment. Therefore, complete cure of HIV needs complete eradication of latent reservoirs.
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Affiliation(s)
- Areej Alshorman
- Department of Mathematics, University of Michigan, Ann Arbor, MI, USA
| | | | - Trachette Jackson
- Department of Mathematics, University of Michigan, Ann Arbor, MI, USA
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Almehmadi MM, Shafie AA, Allahyani M, Muhammad T, Baammi S, Aljuaid A, Almalki AA, Alsaiari AA, Ashour AA. Identification of human immunodeficiency virus -1 E protein-targeting lead compounds by pharmacophore based screening. Saudi Med J 2022; 43:1324-1332. [PMID: 36517066 PMCID: PMC9994525 DOI: 10.15537/smj.2022.43.12.20220599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 11/17/2022] [Indexed: 12/17/2023] Open
Abstract
OBJECTIVES To identify potential compounds by seeking the knowledge of molecular interactions between human immunodeficiency virus (HIV) glycoprotein (gp) 120 protein and anti-HIV drug (BMS-488043). METHODS This study is a computational structure-based drug design study, carried out at University of Taif, Saudi Arabia and African Genome Centre (AGC), Mohammed VI Polytechnic University, Benguerir, Morocco from January 2021 to March 2022. Initially, using the docked structure of gp120 with BMS-488043, a structure-based pharmacophore model was created. The generated model was utilized for virtual screening of the ZINC and ChemBridge database in order to identify hit compounds. To further assess the time-dependent stability of the selected complexes, computer simulation was performed. RESULTS From pharmacophore-based screening, 356 hits were obtained from both the database. The docking studies of the retrieved hit compounds reveal that all the compounds fit into the binding site of gp120. However, based on the significant interactions with the crucial residues and docking scores four compounds were suggested as potential hits. MD simulation of ChemBridge14695864 and ZINC06893293 in complex with gp120 suggested that both compounds significantly stabilized the receptor. CONCLUSION These findings could aid in the design of effective drugs against HIV by inhibiting the interaction between gp120 and CD4.
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Affiliation(s)
- Mazen M. Almehmadi
- From the Department of Clinical Laboratory Sciences (Almehmadi, Shafie, Allahyani, Aljuaid, Almalki, Alsaiari), College of Applied Medical Sciences, and from the Department of Oral (Ashour), Maxillofacial Surgery and Diagnostic Sciences, Faculty of Dentistry, Taif University, Taif, Kingdom of Saudi Arabia; from the Molecular Neuropsychiatry & Development (MiND) Lab (Muhammad), Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Canada; and from the African Genome Centre (Baammi), Mohammad VI Polytechnic University, Benguerir, Morocco.
| | - Alaa A. Shafie
- From the Department of Clinical Laboratory Sciences (Almehmadi, Shafie, Allahyani, Aljuaid, Almalki, Alsaiari), College of Applied Medical Sciences, and from the Department of Oral (Ashour), Maxillofacial Surgery and Diagnostic Sciences, Faculty of Dentistry, Taif University, Taif, Kingdom of Saudi Arabia; from the Molecular Neuropsychiatry & Development (MiND) Lab (Muhammad), Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Canada; and from the African Genome Centre (Baammi), Mohammad VI Polytechnic University, Benguerir, Morocco.
| | - Mamdouh Allahyani
- From the Department of Clinical Laboratory Sciences (Almehmadi, Shafie, Allahyani, Aljuaid, Almalki, Alsaiari), College of Applied Medical Sciences, and from the Department of Oral (Ashour), Maxillofacial Surgery and Diagnostic Sciences, Faculty of Dentistry, Taif University, Taif, Kingdom of Saudi Arabia; from the Molecular Neuropsychiatry & Development (MiND) Lab (Muhammad), Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Canada; and from the African Genome Centre (Baammi), Mohammad VI Polytechnic University, Benguerir, Morocco.
| | - Tahir Muhammad
- From the Department of Clinical Laboratory Sciences (Almehmadi, Shafie, Allahyani, Aljuaid, Almalki, Alsaiari), College of Applied Medical Sciences, and from the Department of Oral (Ashour), Maxillofacial Surgery and Diagnostic Sciences, Faculty of Dentistry, Taif University, Taif, Kingdom of Saudi Arabia; from the Molecular Neuropsychiatry & Development (MiND) Lab (Muhammad), Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Canada; and from the African Genome Centre (Baammi), Mohammad VI Polytechnic University, Benguerir, Morocco.
| | - Soukayna Baammi
- From the Department of Clinical Laboratory Sciences (Almehmadi, Shafie, Allahyani, Aljuaid, Almalki, Alsaiari), College of Applied Medical Sciences, and from the Department of Oral (Ashour), Maxillofacial Surgery and Diagnostic Sciences, Faculty of Dentistry, Taif University, Taif, Kingdom of Saudi Arabia; from the Molecular Neuropsychiatry & Development (MiND) Lab (Muhammad), Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Canada; and from the African Genome Centre (Baammi), Mohammad VI Polytechnic University, Benguerir, Morocco.
| | - Abdulelah Aljuaid
- From the Department of Clinical Laboratory Sciences (Almehmadi, Shafie, Allahyani, Aljuaid, Almalki, Alsaiari), College of Applied Medical Sciences, and from the Department of Oral (Ashour), Maxillofacial Surgery and Diagnostic Sciences, Faculty of Dentistry, Taif University, Taif, Kingdom of Saudi Arabia; from the Molecular Neuropsychiatry & Development (MiND) Lab (Muhammad), Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Canada; and from the African Genome Centre (Baammi), Mohammad VI Polytechnic University, Benguerir, Morocco.
| | - Abdulraheem A. Almalki
- From the Department of Clinical Laboratory Sciences (Almehmadi, Shafie, Allahyani, Aljuaid, Almalki, Alsaiari), College of Applied Medical Sciences, and from the Department of Oral (Ashour), Maxillofacial Surgery and Diagnostic Sciences, Faculty of Dentistry, Taif University, Taif, Kingdom of Saudi Arabia; from the Molecular Neuropsychiatry & Development (MiND) Lab (Muhammad), Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Canada; and from the African Genome Centre (Baammi), Mohammad VI Polytechnic University, Benguerir, Morocco.
| | - Ahad Amer Alsaiari
- From the Department of Clinical Laboratory Sciences (Almehmadi, Shafie, Allahyani, Aljuaid, Almalki, Alsaiari), College of Applied Medical Sciences, and from the Department of Oral (Ashour), Maxillofacial Surgery and Diagnostic Sciences, Faculty of Dentistry, Taif University, Taif, Kingdom of Saudi Arabia; from the Molecular Neuropsychiatry & Development (MiND) Lab (Muhammad), Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Canada; and from the African Genome Centre (Baammi), Mohammad VI Polytechnic University, Benguerir, Morocco.
| | - Amal Adnan Ashour
- From the Department of Clinical Laboratory Sciences (Almehmadi, Shafie, Allahyani, Aljuaid, Almalki, Alsaiari), College of Applied Medical Sciences, and from the Department of Oral (Ashour), Maxillofacial Surgery and Diagnostic Sciences, Faculty of Dentistry, Taif University, Taif, Kingdom of Saudi Arabia; from the Molecular Neuropsychiatry & Development (MiND) Lab (Muhammad), Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Canada; and from the African Genome Centre (Baammi), Mohammad VI Polytechnic University, Benguerir, Morocco.
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5
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Vivekanandan S, Vetrivel U, Hanna LE. Design of human immunodeficiency virus-1 neutralizing peptides targeting CD4-binding site: An integrative computational biologics approach. Front Med (Lausanne) 2022; 9:1036874. [DOI: 10.3389/fmed.2022.1036874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 10/26/2022] [Indexed: 11/19/2022] Open
Abstract
Peptide therapeutics have recently gained momentum in antiviral therapy due to their increased potency and cost-effectiveness. Interaction of the HIV-1 envelope gp120 with the host CD4 receptor is a critical step for viral entry, and therefore the CD4-binding site (CD4bs) of gp120 is a potential hotspot for blocking HIV-1 infection. The present study aimed to design short peptides from well-characterized CD4bs targeting broadly neutralizing antibodies (bNAbs), which could be utilized as bNAb mimetics for viral neutralization. Co-crystallized structures of HIV-1 gp120 in complex with CD4bs-directed bNAbs were used to derive hexameric peptides using the Rosetta Peptiderive protocol. Based on empirical insights into co-crystallized structures, peptides derived from the heavy chain alone were considered. The peptides were docked with both HIV-1 subtype B and C gp120, and the stability of the peptide–antigen complexes was validated using extensive Molecular Dynamics (MD) simulations. Two peptides identified in the study demonstrated stable intermolecular interactions with SER365, GLY366, and GLY367 of the PHE43 cavity in the CD4 binding pocket, and with ASP368 of HIV-1 gp120, thereby mimicking the natural interaction between ASP368gp120 and ARG59CD4–RECEPTOR. Furthermore, the peptides featured favorable physico-chemical properties for virus neutralization suggesting that these peptides may be highly promising bNAb mimetic candidates that may be taken up for experimental validation.
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6
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Kurkin AV, Curreli F, Iusupov IR, Spiridonov EA, Ahmed S, Markov PO, Manasova EV, Altieri A, Debnath AK. Design, Synthesis, and Antiviral Activity of the Thiazole Positional Isomers of a Potent HIV-1 Entry Inhibitor NBD-14270. ChemMedChem 2022; 17:e202200344. [PMID: 36097139 DOI: 10.1002/cmdc.202200344] [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: 06/30/2022] [Revised: 09/12/2022] [Indexed: 01/14/2023]
Abstract
The envelope glycoprotein gp120 of human immunodeficiency virus type 1 (HIV-1) plays a critical role in virus entry to the cells by binding to the host cellular protein CD4. Earlier, we reported the design and discovery of a series of highly potent small-molecule entry antagonists containing a thiazole ring (Scaffold A). Since this thiazole ring connected with an ethyl amide linkage represents the molecule's flexible part, we decided to explore substituting Scaffold A with two other positional isomers of the thiazole ring (Scaffold B and C) to evaluate their effect on the antiviral potency and cellular toxicity. Here we report the novel synthesis of two sets of positional thiazole isomers of the NBD-14270 by retrosynthetic analysis approach, their anti-HIV-1 activity, cellular toxicity, and structure-activity relationships. The study revealed that Scaffold A provided the best HIV-1 inhibitors with higher potency and better selectivity index (SI).
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Affiliation(s)
| | - Francesca Curreli
- Laboratory of Molecular Modeling & Drug Design, Lindsley F. Kimball Research Institute, New York Blood Center, 310 E 67th Street, New York, NY 10065, USA
| | - Ildar R Iusupov
- EDASA Scientific srls, Via Stingi 37, 66050, San Salvo (CH), Italy
| | | | - Shahad Ahmed
- Laboratory of Molecular Modeling & Drug Design, Lindsley F. Kimball Research Institute, New York Blood Center, 310 E 67th Street, New York, NY 10065, USA
| | - Pavel O Markov
- EDASA Scientific srls, Via Stingi 37, 66050, San Salvo (CH), Italy
| | | | - Andrea Altieri
- EDASA Scientific srls, Via Stingi 37, 66050, San Salvo (CH), Italy
| | - Asim K Debnath
- Laboratory of Molecular Modeling & Drug Design, Lindsley F. Kimball Research Institute, New York Blood Center, 310 E 67th Street, New York, NY 10065, USA
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7
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Palabindela R, Guda R, Ramesh G, Bodapati R, Nukala SK, Myadaraveni P, Ravi G, Kasula M. Curcumin based Pyrazole-thiazole Hybrids as Antiproliferative Agents: Synthesis, Pharmacokinetic, Photophysical Properties, and Docking Studies. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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8
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Deng C, Yan H, Wang J, Liu BS, Liu K, Shi YM. The anti-HIV potential of imidazole, oxazole and thiazole hybrids: A mini-review. ARAB J CHEM 2022. [DOI: 10.1016/j.arabjc.2022.104242] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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9
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Comparative Pharmacokinetics of a Dual Inhibitor of HIV-1, NBD-14189, in Rats and Dogs with a Proof-of-Concept Evaluation of Antiviral Potency in SCID-hu Mouse Model. Viruses 2022; 14:v14102268. [PMID: 36298823 PMCID: PMC9611370 DOI: 10.3390/v14102268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/12/2022] [Accepted: 10/13/2022] [Indexed: 11/16/2022] Open
Abstract
We earlier reported substantial progress in designing gp120 antagonists. Notably, we discovered that NBD-14189 is not only the most active gp120 antagonist but also shows antiviral activity against HIV-1 Reverse Transcriptase (RT). We also confirmed its binding to HIV-1 RT by X-ray crystallography. The dual inhibition is highly significant because, intriguingly, this compound bridges the dNTP and NNRTI-binding sites and inhibits the polymerase activity of isolated RT in the enzymatic assay. This novel finding is expected to lead to new avenues in designing a novel class of HIV-1 dual inhibitors. Therefore, we needed to advance this inhibitor to preclinical assessment. To this end, we report the pharmacokinetics (PK) study of NBD-14189 in rats and dogs. Subsequently, we assessed the toxicity and therapeutic efficacy in vivo in the SCID-hu Thy/Liv mouse model. The PK data indicated a favorable half-life (t1/2) and excellent oral bioavailability (%F = 61%). NBD-14189 did not show any measurable toxicity in the mice, and treatment reduced HIV replication at 300 mg/kg per day in the absence of clear evidence of protection from HIV-mediated human thymocyte depletion. The data indicated the potential of this inhibitor as an anti-HIV-1 agent and needs to be assessed in a non-human primate (NHP) model.
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10
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K. F, C. G. A, Shyam P, Gondru R, Banothu J. 1,2,3-Triazole Linked Chalcone-Morpholine Hybrids: Synthesis, In Vitro Antibacterial Evaluation and In Silico ADMET Predictions. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2130369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Fabitha K.
- Department of Chemistry, National Institute of Technology Calicut, Kozhikode, India
| | - Arya C. G.
- Department of Chemistry, National Institute of Technology Calicut, Kozhikode, India
| | - Perugu Shyam
- Department of Biotechnology, National Institute of Technology Warangal, Warangal, India
| | - Ramesh Gondru
- Environmental Monitoring & Exposure Assessment (Air) Laboratory, ICMR-NIREH, Bhopal, India
| | - Janardhan Banothu
- Department of Chemistry, National Institute of Technology Calicut, Kozhikode, India
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Jiang S, Tuzikov A, Andrianov A. Small-molecule HIV-1 entry inhibitors targeting the epitopes of broadly neutralizing antibodies. Cell Chem Biol 2022; 29:757-773. [PMID: 35353988 DOI: 10.1016/j.chembiol.2022.03.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 01/27/2022] [Accepted: 03/10/2022] [Indexed: 11/20/2022]
Abstract
Highly active antiretroviral therapy currently used for HIV/AIDS has significantly increased the life expectancy of HIV-infected individuals. It has also improved the quality of life, reduced mortality, and decreased the incidence of AIDS and HIV-related conditions. Currently, however, affected individuals are typically on a lifetime course of several therapeutic drugs, all with the potential for associated toxicity and emergence of resistance. This calls for development of novel, potent, and broad anti-HIV agents able to stop the spread of HIV/AIDS. Significant progress has been made toward identification of anti-HIV-1 broadly neutralizing antibodies (bNAbs). However, antibody-based drugs are costly to produce and store. Administration (by injection only) and other obstacles limit clinical use. In recent years, several highly promising small-molecule HIV-1 entry inhibitors targeting the epitopes of bNAbs have been developed. These newly developed compounds are the focus of the present article.
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Affiliation(s)
- Shibo Jiang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Institute of Infectious Diseases and Biosecurity, Fudan University, Shanghai 200032, China.
| | - Alexander Tuzikov
- United Institute of Informatics Problems, National Academy of Sciences of Belarus, 220012 Minsk, Republic of Belarus
| | - Alexander Andrianov
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, 220141 Minsk, Republic of Belarus.
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12
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Moghadam ES, Mireskandari K, Abdel-Jalil R, Amini M. An approach to pharmacological targets of pyrrole family from a medicinal chemistry viewpoint. Mini Rev Med Chem 2022; 22:2486-2561. [PMID: 35339175 DOI: 10.2174/1389557522666220325150531] [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: 11/27/2021] [Revised: 01/12/2022] [Accepted: 01/30/2022] [Indexed: 11/22/2022]
Abstract
Pyrrole is one of the most widely used heterocycles in the pharmaceutical industry. Due to the importance of pyrrole structure in drug design and development, herein, we tried to conduct an extensive review of the bioactive pyrrole based compounds reported recently. The bioactivity of pyrrole derivatives varies, so in the review, we categorized them based on their direct pharmacologic targets. Therefore, readers are able to find the variety of biologic targets for pyrrole containing compounds easily. This review explains around seventy different biologic targets for pyrrole based derivatives, so, it is helpful for medicinal chemists in design and development novel bioactive compounds for different diseases. This review presents an extensive meaningful structure activity relationship for each reported structure as much as possible. The review focuses on papers published between 2018 and 2020.
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Affiliation(s)
- Ebrahim Saeedian Moghadam
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran14176, Iran.
- The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran.
- Department of Chemistry, College of Science, Sultan Qaboos University, Muscat, P.O. Box 36, P.C. 123, Sultanate of Oman
| | - Katayoon Mireskandari
- Department of Pharmaceutics, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran 1417614411, Iran
| | - Raid Abdel-Jalil
- Department of Chemistry, College of Science, Sultan Qaboos University, Muscat, P.O. Box 36, P.C. 123, Sultanate of Oman
| | - Mohsen Amini
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran14176, Iran.
- The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran
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Small-Molecule HIV Entry Inhibitors Targeting gp120 and gp41. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1366:27-43. [DOI: 10.1007/978-981-16-8702-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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14
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Gao ZY, He Y, Li LY, Tian JS, Loh TP. BF 3-promoted reactions of α-amino acetals with alkynes to 2,5-disubstituted pyrroles. Org Chem Front 2022. [DOI: 10.1039/d2qo00405d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An efficient BF3-promoted cyclization of α-amino acetals with alkynes for the assembly of substituted pyrroles has been developed. This cascade process can be easily achieved through a simple metal-free operation under mild conditions.
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Affiliation(s)
- Zhi-Yuan Gao
- School of Chemistry and Molecular Engineering, Nanjing Tech University (NanjingTech), Nanjing 211816, P. R. China
| | - Yu He
- School of Chemistry and Molecular Engineering, Nanjing Tech University (NanjingTech), Nanjing 211816, P. R. China
| | - Lan-Yang Li
- School of Chemistry and Molecular Engineering, Nanjing Tech University (NanjingTech), Nanjing 211816, P. R. China
| | - Jie-Sheng Tian
- School of Chemistry and Chemical Engineering, Northwestern Polytechnical University (NPU), Xi'an 710072, China
| | - Teck-Peng Loh
- School of Chemistry and Molecular Engineering, Nanjing Tech University (NanjingTech), Nanjing 211816, P. R. China
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371
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15
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The Genesis and Future Prospects of Small Molecule HIV-1 Attachment Inhibitors. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1366:45-64. [DOI: 10.1007/978-981-16-8702-0_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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16
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Recent research results have converted gp120 binders to a therapeutic option for the treatment of HIV-1 infection. A medicinal chemistry point of view. Eur J Med Chem 2021; 229:114078. [PMID: 34992041 DOI: 10.1016/j.ejmech.2021.114078] [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: 11/19/2021] [Revised: 12/16/2021] [Accepted: 12/22/2021] [Indexed: 11/21/2022]
Abstract
Current therapeutic armamentarium for treatment of HIV-1 infection is based on the use of highly active antiretroviral therapy that, unfortunately, does not act as a curative remedy. Moreover, duration of the therapy often results in lack of compliance with the consequent emergence of multidrug resistance. Finally, drug toxicity issues also arise during treatments. In the attempt to achieve a curative effect, in addition to invest substantial resources in finding new anti-HIV-1 agents and in optimizing antiviral lead compounds and drugs currently available, additional efforts should be done to deplete viral reservoir located within host CD4+ T cells. Gp120 binders represent a class of compounds able to affect the interactions between viral envelope proteins and host CD4, thus avoiding virus-to-cell attachment and fusion, and the consequent viral entry into host cells. This review summarizes the efforts done in the last five years to design new gp120 binders, that finally culminated in the approval of fostemsavir as an anti-HIV-1 drug.
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17
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Losada N, Ruiz FX, Curreli F, Gruber K, Pilch A, Das K, Debnath AK, Arnold E. HIV-1 gp120 Antagonists Also Inhibit HIV-1 Reverse Transcriptase by Bridging the NNRTI and NRTI Sites. J Med Chem 2021; 64:16530-16540. [PMID: 34735153 PMCID: PMC10655131 DOI: 10.1021/acs.jmedchem.1c01104] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
HIV-1 infection is typically treated using ≥2 drugs, including at least one HIV-1 reverse transcriptase (RT) inhibitor. Drugs targeting RT comprise nucleos(t)ide RT inhibitors (NRTIs) and non-nucleoside RT inhibitors (NNRTIs). NRTI-triphosphates bind at the polymerase active site and, following incorporation, inhibit DNA elongation. NNRTIs bind at an allosteric pocket ∼10 Å away from the polymerase active site. This study focuses on compounds ("NBD derivatives") originally developed to bind to HIV-1 gp120, some of which inhibit RT. We have determined crystal structures of three NBD compounds in complex with HIV-1 RT, correlating with RT enzyme inhibition and antiviral activity, to develop structure-activity relationships. Intriguingly, these compounds bridge the dNTP and NNRTI-binding sites and inhibit the polymerase activity of RT in the enzymatic assays (IC50 < 5 μM). Two of the lead compounds, NBD-14189 and NBD-14270, show potent antiviral activity (EC50 < 200 nM), and NBD-14270 shows low cytotoxicity (CC50 > 100 μM).
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Affiliation(s)
- Natalie Losada
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, 08854, USA
| | - Francesc X. Ruiz
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, 08854, USA
| | - Francesca Curreli
- Laboratory of Molecular Modeling & Drug Design, Lindsley F. Kimball Research Institute, New York Blood Center, New York, 10065, USA
| | - Kevin Gruber
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, 08854, USA
| | - Alyssa Pilch
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, 08854, USA
| | - Kalyan Das
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, 08854, USA
| | - Asim K. Debnath
- Laboratory of Molecular Modeling & Drug Design, Lindsley F. Kimball Research Institute, New York Blood Center, New York, 10065, USA
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, 08854, USA
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18
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Pyrroles as Privileged Scaffolds in the Search for New Potential HIV Inhibitors. Pharmaceuticals (Basel) 2021; 14:ph14090893. [PMID: 34577593 PMCID: PMC8468532 DOI: 10.3390/ph14090893] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 02/04/2023] Open
Abstract
Acquired immunodeficiency syndrome (AIDS) is caused by human immunodeficiency virus (HIV) and remains a global health problem four decades after the report of its first case. Despite success in viral load suppression and the increase in patient survival due to combined antiretroviral therapy (cART), the development of new drugs has become imperative due to strains that have become resistant to antiretrovirals. In this context, there has been a continuous search for new anti-HIV agents based on several chemical scaffolds, including nitrogenated heterocyclic pyrrole rings, which have been included in several compounds with antiretroviral activity. Thus, this review aims to describe pyrrole-based compounds with anti-HIV activity as a new potential treatment against AIDS, covering the period between 2015 and 2020. Our research allowed us to conclude that pyrrole derivatives are still worth exploring, as they may provide highly active compounds targeting different steps of the HIV-1 replication cycle and act with an innovative mechanism.
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19
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Iusupov IR, Curreli F, Spiridonov EA, Markov PO, Ahmed S, Belov DS, Manasova EV, Altieri A, Kurkin AV, Debnath AK. Design of gp120 HIV-1 entry inhibitors by scaffold hopping via isosteric replacements. Eur J Med Chem 2021; 224:113681. [PMID: 34246921 DOI: 10.1016/j.ejmech.2021.113681] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 06/28/2021] [Accepted: 06/29/2021] [Indexed: 10/20/2022]
Abstract
We present the development of alternative scaffolds and validation of their synthetic pathways as a tool for the exploration of new HIV gp120 inhibitors based on the recently discovered inhibitor of this class, NBD-14136. The new synthetic routes were based on isosteric replacements of the amine and acid precursors required for the synthesis of NBD-14136, guided by molecular modeling and chemical feasibility analysis. To ensure that these synthetic tools and new scaffolds had the potential for further exploration, we eventually tested few representative compounds from each newly designed scaffold against the gp120 inhibition assay and cell viability assays.
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Affiliation(s)
- Ildar R Iusupov
- EDASA Scientific, Scientific Campus, Moscow State University, Leninskie Gory Bld. 75, 77-101b, Moscow, 119992, Russia
| | - Francesca Curreli
- Laboratory of Molecular Modeling & Drug Design, Lindsley F. Kimball Research Institute, New York Blood Center, 310 E 67th Street, New York, 10065, New York, United States
| | - Evgeniy A Spiridonov
- EDASA Scientific, Scientific Campus, Moscow State University, Leninskie Gory Bld. 75, 77-101b, Moscow, 119992, Russia
| | - Pavel O Markov
- EDASA Scientific, Scientific Campus, Moscow State University, Leninskie Gory Bld. 75, 77-101b, Moscow, 119992, Russia
| | - Shahad Ahmed
- Laboratory of Molecular Modeling & Drug Design, Lindsley F. Kimball Research Institute, New York Blood Center, 310 E 67th Street, New York, 10065, New York, United States
| | - Dmitry S Belov
- EDASA Scientific, Scientific Campus, Moscow State University, Leninskie Gory Bld. 75, 77-101b, Moscow, 119992, Russia
| | - Ekaterina V Manasova
- EDASA Scientific, Scientific Campus, Moscow State University, Leninskie Gory Bld. 75, 77-101b, Moscow, 119992, Russia
| | - Andrea Altieri
- EDASA Scientific, Scientific Campus, Moscow State University, Leninskie Gory Bld. 75, 77-101b, Moscow, 119992, Russia.
| | - Alexander V Kurkin
- EDASA Scientific, Scientific Campus, Moscow State University, Leninskie Gory Bld. 75, 77-101b, Moscow, 119992, Russia.
| | - Asim K Debnath
- Laboratory of Molecular Modeling & Drug Design, Lindsley F. Kimball Research Institute, New York Blood Center, 310 E 67th Street, New York, 10065, New York, United States.
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20
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Chandra I, Prabhu SV, Nayak C, Singh SK. E-pharmacophore based screening to identify potential HIV-1 gp120 and CD4 interaction blockers for wild and mutant types. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2021; 32:353-377. [PMID: 33832362 DOI: 10.1080/1062936x.2021.1901310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 03/07/2021] [Indexed: 06/12/2023]
Abstract
HIV-1 gp120 provides a multistage viral entry process through the conserved CD4 binding site. Hunting of potential blockers can diminish the interaction of gp120 with the CD4 host receptor leading to the suppression of HIV-1 infection. Structure-based pharmacophore virtual screening followed by binding free energy calculation, molecular dynamics (MD) simulation and density functional theory (DFT) calculation is applied to discriminate the potential blockers from six small molecule databases. Five compounds from six databases exhibited vital interactions with key residues ASP368, GLU370, ASN425, MET426, TRP427 and GLY473 of gp120, involved in the binding with CD4, host receptor. Most importantly, compound NCI-254200 displayed strong communication with key residues of wild type and drug resistance single mutant gp120 (M426L and W427V) even in the dynamic condition, evidenced from MD simulation. This investigation provided a potential compound NCI-254200 which may show inhibitory activity against HIV-1 gp120 variant interactions with CD4 host cell receptors.
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Affiliation(s)
- I Chandra
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, India
| | - S V Prabhu
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, India
| | - C Nayak
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, India
| | - S K Singh
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, India
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21
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Andrianov AM, Nikolaev GI, Shuldov NA, Bosko IP, Anischenko AI, Tuzikov AV. Application of deep learning and molecular modeling to identify small drug-like compounds as potential HIV-1 entry inhibitors. J Biomol Struct Dyn 2021; 40:7555-7573. [PMID: 33855929 DOI: 10.1080/07391102.2021.1905559] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
A generative adversarial autoencoder for the rational design of potential HIV-1 entry inhibitors able to block CD4-binding site of the viral envelope protein gp120 was developed. To do this, the following studies were carried out: (i) an autoencoder architecture was constructed; (ii) a virtual compound library of potential anti-HIV-1 agents for training the neural network was formed by the concept of click chemistry allowing one to generate a large number of drug candidates by their assembly from small modular units; (iii) molecular docking of all compounds from this library with gp120 was made and calculations of the values of binding free energy were performed; (iv) molecular fingerprints of chemical compounds from the training dataset were generated; (v) training of the developed autoencoder was implemented followed by the validation of this neural network using more than 21 million molecules from the ZINC15 database. As a result, three small drug-like compounds that exhibited the high-affinity binding to gp120 were identified. According to the data from molecular docking, machine learning, quantum chemical calculations, and molecular dynamics simulations, these compounds show the low values of binding free energy in the complexes with gp120 similar to those calculated using the same computational protocols for the HIV-1 entry inhibitors NBD-11021 and NBD-14010, highly potent and broad anti-HIV-1 agents presenting a new generation of the viral CD4 antagonists. The identified CD4-mimetic candidates are suggested to present good scaffolds for the design of novel antiviral drugs inhibiting the early stages of HIV-1 infection.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Alexander M Andrianov
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Republic of Belarus
| | - Grigory I Nikolaev
- United Institute of Informatics Problems, National Academy of Sciences of Belarus, Minsk, Republic of Belarus
| | - Nikita A Shuldov
- Faculty of Applied Mathematics & Computer Science, Belarusian State University, Minsk, Republic of Belarus
| | - Ivan P Bosko
- United Institute of Informatics Problems, National Academy of Sciences of Belarus, Minsk, Republic of Belarus
| | - Arseny I Anischenko
- Faculty of Applied Mathematics & Computer Science, Belarusian State University, Minsk, Republic of Belarus
| | - Alexander V Tuzikov
- United Institute of Informatics Problems, National Academy of Sciences of Belarus, Minsk, Republic of Belarus
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22
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Chang CK, Lin SM, Satange R, Lin SC, Sun SC, Wu HY, Kehn-Hall K, Hou MH. Targeting protein-protein interaction interfaces in COVID-19 drug discovery. Comput Struct Biotechnol J 2021; 19:2246-2255. [PMID: 33936565 PMCID: PMC8064971 DOI: 10.1016/j.csbj.2021.04.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/30/2021] [Accepted: 04/01/2021] [Indexed: 02/06/2023] Open
Abstract
To date, the COVID-19 pandemic has claimed over 1 million human lives, infected another 50 million individuals and wreaked havoc on the global economy. The crisis has spurred the ongoing development of drugs targeting its etiological agent, the SARS-CoV-2. Targeting relevant protein-protein interaction interfaces (PPIIs) is a viable paradigm for the design of antiviral drugs and enriches the targetable chemical space by providing alternative targets for drug discovery. In this review, we will provide a comprehensive overview of the theory, methods and applications of PPII-targeted drug development towards COVID-19 based on recent literature. We will also highlight novel developments, such as the successful use of non-native protein-protein interactions as targets for antiviral drug screening. We hope that this review may serve as an entry point for those interested in applying PPIIs towards COVID-19 drug discovery and speed up drug development against the pandemic.
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Affiliation(s)
- Chung-Ke Chang
- Taiwan Biobank, Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Shan-Meng Lin
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan
| | - Roshan Satange
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan.,Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung 402, Taiwan
| | - Shih-Chao Lin
- Bachelor Degree Program in Marine Biotechnology, National Taiwan Ocean University, Keelung 20224, Taiwan
| | - Sin-Cih Sun
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan
| | - Hung-Yi Wu
- Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan
| | - Kylene Kehn-Hall
- Department of Biomedical Sciences & Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Virginia 24061, United States
| | - Ming-Hon Hou
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan.,Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung 402, Taiwan
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23
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Adamovich SN, Sadykov EK, Ushakov IA, Oborina EN, Belovezhets LA. Antibacterial activity of new silatrane pyrrole-2-carboxamide hybrids. MENDELEEV COMMUNICATIONS 2021. [DOI: 10.1016/j.mencom.2021.03.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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24
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Curreli F, Ahmed S, Benedict Victor SM, Iusupov IR, Spiridonov EA, Belov DS, Altieri A, Kurkin AV, Debnath AK. Design, synthesis, and antiviral activity of a series of CD4-mimetic small-molecule HIV-1 entry inhibitors. Bioorg Med Chem 2021; 32:116000. [PMID: 33461144 DOI: 10.1016/j.bmc.2021.116000] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 12/31/2020] [Indexed: 11/28/2022]
Abstract
We presented our continuing stride to optimize the second-generation NBD entry antagonist targeted to the Phe43 cavity of HIV-1 gp120. We have synthesized thirty-eight new and novel analogs of NBD-14136, earlier designed based on a CH2OH "positional switch" hypothesis, and derived a comprehensive SAR. The antiviral data confirmed that the linear alcohol towards the "N" (C4) of the thiazole ring yielded more active inhibitors than those towards the "S" (C5) of the thiazole ring. The best inhibitor, NBD-14273 (compound 13), showed both improved antiviral activity and selectivity index (SI) against HIV-1HXB2 compared to NBD-14136. We also tested NBD-14273 against a large panel of 50 HIV-1 Env-pseudotyped viruses representing clinical isolates of diverse subtypes. The overall mean data indicate that antiviral potency against these isolates improved by ~3-fold, and SI also improved ~3-fold compared to NBD-14136. This new and novel inhibitor is expected to pave the way for further optimization to a more potent and clinically relevant inhibitor against HIV-1.
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Affiliation(s)
- Francesca Curreli
- Laboratory of Molecular Modeling & Drug Design, Lindsley F. Kimball Research Institute, New York Blood Center, 310 E 67th Street, New York, NY 10065, USA
| | - Shahad Ahmed
- Laboratory of Molecular Modeling & Drug Design, Lindsley F. Kimball Research Institute, New York Blood Center, 310 E 67th Street, New York, NY 10065, USA
| | - Sofia M Benedict Victor
- Laboratory of Molecular Modeling & Drug Design, Lindsley F. Kimball Research Institute, New York Blood Center, 310 E 67th Street, New York, NY 10065, USA
| | - Ildar R Iusupov
- EDASA Scientific, Scientific Park, Moscow State University, Leninskie Gory Bld. 75, 77-101b, 119992 Moscow, Russia
| | - Evgeny A Spiridonov
- EDASA Scientific, Scientific Park, Moscow State University, Leninskie Gory Bld. 75, 77-101b, 119992 Moscow, Russia
| | - Dmitry S Belov
- EDASA Scientific, Scientific Park, Moscow State University, Leninskie Gory Bld. 75, 77-101b, 119992 Moscow, Russia
| | - Andrea Altieri
- EDASA Scientific, Scientific Park, Moscow State University, Leninskie Gory Bld. 75, 77-101b, 119992 Moscow, Russia
| | - Alexander V Kurkin
- EDASA Scientific, Scientific Park, Moscow State University, Leninskie Gory Bld. 75, 77-101b, 119992 Moscow, Russia
| | - Asim K Debnath
- Laboratory of Molecular Modeling & Drug Design, Lindsley F. Kimball Research Institute, New York Blood Center, 310 E 67th Street, New York, NY 10065, USA.
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25
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Rana M, Arif R, Khan FI, Maurya V, Singh R, Faizan MI, Yasmeen S, Dar SH, Alam R, Sahu A, Ahmad T, Rahisuddin. Pyrazoline analogs as potential anticancer agents and their apoptosis, molecular docking, MD simulation, DNA binding and antioxidant studies. Bioorg Chem 2021; 108:104665. [PMID: 33571809 DOI: 10.1016/j.bioorg.2021.104665] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 12/08/2020] [Accepted: 01/16/2021] [Indexed: 12/12/2022]
Abstract
N-formyl pyrazoline derivatives (3a-3l) were designed and synthesized via Michael addition reaction through cyclization of chalcones with hydrazine hydrate in presence of formic acid. The structural elucidation of N-formyl pyrazoline derivatives was carried out by various spectroscopic techniques such as 1H, 13C NMR, FT-IR, UV-visible spectroscopy, mass spectrometry and elemental analysis. Anticancer activity of the pyrazoline derivatives (3a-3l) was evaluated against human lung cancer (A549), fibrosarcoma cell lines (HT1080) and human primary normal lung cells (HFL-1) by MTT assay. The results of anticancer activity showed that potent analogs 3b and 3d exhibited promising activity against A549 (IC50 = 12.47 ± 1.08 and 14.46 ± 2.76 µM) and HT1080 (IC50 = 11.40 ± 0.66 and 23.74 ± 13.30 µM) but low toxic against the HFL-1 (IC50 = 116.47 ± 43.38 and 152.36 ± 22.18 µM). The anticancer activity of potent derivatives (3b and 3d) against A549 cancer cell line was further confirmed by flow cytometry based approach. DNA binding interactions of the pyrazoline derivatives 3b and 3d have been carried out with calf thymus DNA (Ct-DNA) using absorption, fluorescence and viscosity measurements, circular dichroism and cyclic voltammetry. Antioxidant potential of N-formyl pyrazoline derivatives (3a-3l) has been also estimated through DPPH (2,2-diphenyl-1-picrylhydrazyl) free radical and H2O2. Results revealed that all the compounds exhibited significant antioxidant activity. In silico molecular modelling and ADMET properties of pyrazoline derivatives were also studied using PyRx software against topoisomerase II receptor with PDB ID: 1ZXM to explore their best hits. MD simulation of 3b and 3d was also carried out with topoisomerase II for structure-function correlation in a protein. HuTopoII inhibitory activity of the analogs (3a-3l) was examined by relaxation assay at varying concentrations 100-1000 µM.
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Affiliation(s)
- Manish Rana
- Department of Chemistry, Jamia Millia Islamia, New Delhi 110025, India
| | - Rizwan Arif
- Department of Chemistry, Jamia Millia Islamia, New Delhi 110025, India
| | - Faez Iqbal Khan
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, China
| | - Vikas Maurya
- Special Centre for Molecular Medicine, Jawharlal Nehru University, New Delhi 110067, India
| | - Raja Singh
- Special Centre for Molecular Medicine, Jawharlal Nehru University, New Delhi 110067, India
| | - Md Imam Faizan
- Multidisciplinary Centre for Advanced Research & Studies, Jamia Millia Islamia, New Delhi 110025, India
| | - Shama Yasmeen
- Department of Chemistry, Jamia Millia Islamia, New Delhi 110025, India
| | - Sajad Hussain Dar
- Department of Chemistry, Jamia Millia Islamia, New Delhi 110025, India
| | - Raquib Alam
- Department of Applied Sciences, University Polytechnic, Jamia Millia Islamia, New Delhi 110025, India
| | - Ankita Sahu
- ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi 110029, India
| | - Tanveer Ahmad
- Multidisciplinary Centre for Advanced Research & Studies, Jamia Millia Islamia, New Delhi 110025, India
| | - Rahisuddin
- Department of Chemistry, Jamia Millia Islamia, New Delhi 110025, India.
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26
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Pu J, Dai Y, Wang Q, Lu L, Zhang J, Xu W, Xie L, Wang S, Yu F, He X, Jiang S. Rational Design of A Novel Small-Molecule HIV-1 Inactivator Targeting Both gp120 and gp41 of HIV-1. Front Pharmacol 2021; 11:613361. [PMID: 33569006 PMCID: PMC7868322 DOI: 10.3389/fphar.2020.613361] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 12/21/2020] [Indexed: 11/13/2022] Open
Abstract
Virus inactivator can inactivate cell-free virions without relying on their replication cycle, potentially reducing the impact of viral infection on cells. Previously, we successfully constructed a HIV-1 protein inactivator, 2DLT, by conjugating the D1D2 region of CD4 to the fusion inhibitor T1144 via a 35-amino acid linker. Therefore, it targets both the CD4 binding site in gp120 and NHR region in gp41. Considering that small-molecule agents have the advantages of fast production, low cost, good stability, and oral availability, we herein report the design of a new small-molecule HIV-1 inactivator, FD028, by conjugating FD016 (an analog of NBD-556, a gp120-CD4 binding inhibitor) with FD017 (an analog of 11d, an HIV-1 fusion inhibitor). The results showed that FD028 inactivated cell-free virions at a moderate nanomolar concentration by targeting both HIV-1 gp120 and gp41. Moreover, FD028 has broad-spectrum inhibition and inactivation activity against HIV-1 resistant strains and primary isolates of different subtypes without significant cytotoxicity. Therefore, FD028 has potential for further development as an HIV-1 inactivator-based therapeutic.
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Affiliation(s)
- Jing Pu
- Key Laboratory of Medical Molecular Virology of MOE/MOH, School of Basic Medical Sciences & Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.,Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY, United States
| | - Yu Dai
- Beijing Institute of Radiation Medicine, Beijing, China.,College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Qian Wang
- Key Laboratory of Medical Molecular Virology of MOE/MOH, School of Basic Medical Sciences & Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Lu Lu
- Key Laboratory of Medical Molecular Virology of MOE/MOH, School of Basic Medical Sciences & Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Junqi Zhang
- Medical Molecular Virology (MOE/NHC/CAMS), Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wei Xu
- Key Laboratory of Medical Molecular Virology of MOE/MOH, School of Basic Medical Sciences & Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Lan Xie
- Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Shengqi Wang
- Beijing Institute of Radiation Medicine, Beijing, China
| | - Fei Yu
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Xiaoyang He
- Beijing Institute of Radiation Medicine, Beijing, China
| | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology of MOE/MOH, School of Basic Medical Sciences & Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.,Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY, United States
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27
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Neto JSS, Zeni G. Transition Metal‐Catalyzed and Metal‐Free Cyclization Reactions of Alkynes with Nitrogen‐Containing Substrates: Synthesis of Pyrrole Derivatives. ChemCatChem 2020. [DOI: 10.1002/cctc.201902325] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Jose S. S. Neto
- Departamento de QuímicaUniversidade Federal de Santa Catarina Florianópolis Santa Catarina 88040-900 Brazil
| | - Gilson Zeni
- Department of Biochemistry and Molecular Biology Laboratório de Síntese Reatividade Avaliação Farmacológica e Toxicológica de Organocalcogênios, CCNEUniversidade Federal de Santa Maria Santa Maria Rio Grande do Sul 97105-900 Brazil
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28
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Kanwal S, Ann NU, Fatima S, Emwas AH, Alazmi M, Gao X, Ibrar M, Zaib Saleem RS, Chotana GA. Facile Synthesis of NH-Free 5-(Hetero)Aryl-Pyrrole-2-Carboxylates by Catalytic C-H Borylation and Suzuki Coupling. Molecules 2020; 25:molecules25092106. [PMID: 32365945 PMCID: PMC7248765 DOI: 10.3390/molecules25092106] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 04/26/2020] [Accepted: 04/29/2020] [Indexed: 11/25/2022] Open
Abstract
A convenient two-step preparation of NH-free 5-aryl-pyrrole-2-carboxylates is described. The synthetic route consists of catalytic borylation of commercially available pyrrole-2-carboxylate ester followed by Suzuki coupling without going through pyrrole N–H protection and deprotection steps. The resulting 5-aryl substituted pyrrole-2-carboxylates were synthesized in good- to excellent yields. This synthetic route can tolerate a variety of functional groups including those with acidic protons on the aryl bromide coupling partner. This methodology is also applicable for cross-coupling with heteroaryl bromides to yield pyrrole-thiophene, pyrrole-pyridine, and 2,3’-bi-pyrrole based bi-heteroaryls.
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Affiliation(s)
- Saba Kanwal
- Department of Chemistry and Chemical Engineering, Syed Babar Ali School of Science & Engineering (SBASSE), Lahore University of Management Sciences (LUMS), Lahore 54792, Pakistan; (S.K.); (N.-u.-A.); (S.F.); (M.I.); (R.S.Z.S.)
| | - Noor-ul- Ann
- Department of Chemistry and Chemical Engineering, Syed Babar Ali School of Science & Engineering (SBASSE), Lahore University of Management Sciences (LUMS), Lahore 54792, Pakistan; (S.K.); (N.-u.-A.); (S.F.); (M.I.); (R.S.Z.S.)
| | - Saman Fatima
- Department of Chemistry and Chemical Engineering, Syed Babar Ali School of Science & Engineering (SBASSE), Lahore University of Management Sciences (LUMS), Lahore 54792, Pakistan; (S.K.); (N.-u.-A.); (S.F.); (M.I.); (R.S.Z.S.)
| | - Abdul-Hamid Emwas
- Core Labs, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia;
| | - Meshari Alazmi
- Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (M.A.); (X.G.)
- College of Computer Science and Engineering, University of Ha’il, P.O. Box 2440, Ha’il 81481, Saudi Arabia
| | - Xin Gao
- Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (M.A.); (X.G.)
| | - Maha Ibrar
- Department of Chemistry and Chemical Engineering, Syed Babar Ali School of Science & Engineering (SBASSE), Lahore University of Management Sciences (LUMS), Lahore 54792, Pakistan; (S.K.); (N.-u.-A.); (S.F.); (M.I.); (R.S.Z.S.)
| | - Rahman Shah Zaib Saleem
- Department of Chemistry and Chemical Engineering, Syed Babar Ali School of Science & Engineering (SBASSE), Lahore University of Management Sciences (LUMS), Lahore 54792, Pakistan; (S.K.); (N.-u.-A.); (S.F.); (M.I.); (R.S.Z.S.)
| | - Ghayoor Abbas Chotana
- Department of Chemistry and Chemical Engineering, Syed Babar Ali School of Science & Engineering (SBASSE), Lahore University of Management Sciences (LUMS), Lahore 54792, Pakistan; (S.K.); (N.-u.-A.); (S.F.); (M.I.); (R.S.Z.S.)
- Correspondence: ; Tel.: +92-42-3560-8281
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Curreli F, Ahmed S, Benedict Victor SM, Iusupov IR, Belov DS, Markov PO, Kurkin AV, Altieri A, Debnath AK. Preclinical Optimization of gp120 Entry Antagonists as anti-HIV-1 Agents with Improved Cytotoxicity and ADME Properties through Rational Design, Synthesis, and Antiviral Evaluation. J Med Chem 2020; 63:1724-1749. [PMID: 32031803 DOI: 10.1021/acs.jmedchem.9b02149] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We previously reported a milestone in the optimization of NBD-11021, an HIV-1 gp120 antagonist, by developing a new and novel analogue, NBD-14189 (Ref1), which showed antiviral activity against HIV-1HXB2, with a half maximal inhibitory concentration of 89 nM. However, cytotoxicity remained high, and the absorption, distribution, metabolism, and excretion (ADME) data showed relatively poor aqueous solubility. To optimize these properties, we replaced the phenyl ring in the compound with a pyridine ring and synthesized a set of 48 novel compounds. One of the new analogues, NBD-14270 (8), showed a marked improvement in cytotoxicity, with 3-fold and 58-fold improvements in selectivity index value compared with that of Ref1 and NBD-11021, respectively. Furthermore, the in vitro ADME data clearly showed improvements in aqueous solubility and other properties compared with those for Ref1. The data for 8 indicated that the pyridine scaffold is a good bioisostere for phenyl, allowing the further optimization of this molecule.
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Affiliation(s)
- Francesca Curreli
- Laboratory of Molecular Modeling & Drug Design, Lindsley F. Kimball Research Institute , New York Blood Center , 310 E 67th Street , New York 10065 , New York , United States
| | - Shahad Ahmed
- Laboratory of Molecular Modeling & Drug Design, Lindsley F. Kimball Research Institute , New York Blood Center , 310 E 67th Street , New York 10065 , New York , United States
| | - Sofia M Benedict Victor
- Laboratory of Molecular Modeling & Drug Design, Lindsley F. Kimball Research Institute , New York Blood Center , 310 E 67th Street , New York 10065 , New York , United States
| | - Ildar R Iusupov
- EDASA Scientific, Scientific Park , Moscow State University , Leninskie Gory Bld. 75, 77-101b , Moscow 119992 , Russia
| | - Dmitry S Belov
- EDASA Scientific, Scientific Park , Moscow State University , Leninskie Gory Bld. 75, 77-101b , Moscow 119992 , Russia
| | - Pavel O Markov
- EDASA Scientific, Scientific Park , Moscow State University , Leninskie Gory Bld. 75, 77-101b , Moscow 119992 , Russia
| | - Alexander V Kurkin
- EDASA Scientific, Scientific Park , Moscow State University , Leninskie Gory Bld. 75, 77-101b , Moscow 119992 , Russia
| | - Andrea Altieri
- EDASA Scientific, Scientific Park , Moscow State University , Leninskie Gory Bld. 75, 77-101b , Moscow 119992 , Russia
| | - Asim K Debnath
- Laboratory of Molecular Modeling & Drug Design, Lindsley F. Kimball Research Institute , New York Blood Center , 310 E 67th Street , New York 10065 , New York , United States
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Motati DR, Uredi D, Watkins EB. The Discovery and Development of Oxalamide and Pyrrole Small Molecule Inhibitors of gp120 and HIV Entry - A Review. Curr Top Med Chem 2019; 19:1650-1675. [PMID: 31424369 DOI: 10.2174/1568026619666190717163959] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 06/14/2019] [Accepted: 06/25/2019] [Indexed: 02/07/2023]
Abstract
Human immunodeficiency virus type-1 (HIV-1) is the causative agent responsible for the acquired immunodeficiency syndrome (AIDS) pandemic. More than 60 million infections and 25 million deaths have occurred since AIDS was first identified in the early 1980s. Advances in available therapeutics, in particular combination antiretroviral therapy, have significantly improved the treatment of HIV infection and have facilitated the shift from high mortality and morbidity to that of a manageable chronic disease. Unfortunately, none of the currently available drugs are curative of HIV. To deal with the rapid emergence of drug resistance, off-target effects, and the overall difficulty of eradicating the virus, an urgent need exists to develop new drugs, especially against targets critically important for the HIV-1 life cycle. Viral entry, which involves the interaction of the surface envelope glycoprotein, gp120, with the cellular receptor, CD4, is the first step of HIV-1 infection. Gp120 has been validated as an attractive target for anti-HIV-1 drug design or novel HIV detection tools. Several small molecule gp120 antagonists are currently under investigation as potential entry inhibitors. Pyrrole, piperazine, triazole, pyrazolinone, oxalamide, and piperidine derivatives, among others, have been investigated as gp120 antagonist candidates. Herein, we discuss the current state of research with respect to the design, synthesis and biological evaluation of oxalamide derivatives and five-membered heterocycles, namely, the pyrrole-containing small molecule as inhibitors of gp120 and HIV entry.
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Affiliation(s)
- Damoder Reddy Motati
- Department of Pharmaceutical Sciences, Center for Pharmacometrics and Molecular Discovery, College of Pharmacy, Union University, Jackson, Tennessee 38305, United States
| | - Dilipkumar Uredi
- Department of Pharmaceutical Sciences, Center for Pharmacometrics and Molecular Discovery, College of Pharmacy, Union University, Jackson, Tennessee 38305, United States
| | - E Blake Watkins
- Department of Pharmaceutical Sciences, Center for Pharmacometrics and Molecular Discovery, College of Pharmacy, Union University, Jackson, Tennessee 38305, United States
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Suttisintong K, Kaewchangwat N, Thanayupong E, Nerungsi C, Srikun O, Pungpo P. Recent Progress in the Development of HIV-1 Entry Inhibitors: From Small Molecules to Potent Anti-HIV Agents. Curr Top Med Chem 2019; 19:1599-1620. [DOI: 10.2174/1568026619666190712204050] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Revised: 06/07/2019] [Accepted: 06/21/2019] [Indexed: 01/21/2023]
Abstract
Viral entry, the first process in the reproduction of viruses, primarily involves attachment of the viral envelope proteins to membranes of the host cell. The crucial components that play an important role in viral entry include viral surface glycoprotein gp120, viral transmembrane glycoprotein gp41, host cell glycoprotein (CD4), and host cell chemokine receptors (CCR5 and CXCR4). Inhibition of the multiple molecular interactions of these components can restrain viruses, such as HIV-1, from fusion with the host cell, blocking them from reproducing. This review article specifically focuses on the recent progress in the development of small-molecule HIV-1 entry inhibitors and incorporates important aspects of their structural modification that lead to the discovery of new molecular scaffolds with more potency.
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Affiliation(s)
- Khomson Suttisintong
- National Nanotechnology Center (NANOTEC), National Science and Technology, Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Narongpol Kaewchangwat
- National Nanotechnology Center (NANOTEC), National Science and Technology, Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Eknarin Thanayupong
- National Nanotechnology Center (NANOTEC), National Science and Technology, Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Chakkrapan Nerungsi
- The Government Pharmaceutical Organization, 75/1 Rama VI Road, Ratchathewi, Bangkok 10400, Thailand
| | - Onsiri Srikun
- The Government Pharmaceutical Organization, 75/1 Rama VI Road, Ratchathewi, Bangkok 10400, Thailand
| | - Pornpan Pungpo
- Department of Chemistry, Faculty of Science, Ubon Ratchathani University, 85 Sathonlamark Road, Warinchamrap, Ubon Ratchathani 34190, Thailand
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Andrianov AM, Nikolaev GI, Kornoushenko YV, Xu W, Jiang S, Tuzikov AV. In Silico Identification of Novel Aromatic Compounds as Potential HIV-1 Entry Inhibitors Mimicking Cellular Receptor CD4. Viruses 2019; 11:v11080746. [PMID: 31412617 PMCID: PMC6723994 DOI: 10.3390/v11080746] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 07/31/2019] [Accepted: 08/01/2019] [Indexed: 12/13/2022] Open
Abstract
Despite recent progress in the development of novel potent HIV-1 entry/fusion inhibitors, there are currently no licensed antiviral drugs based on inhibiting the critical interactions of the HIV-1 envelope gp120 protein with cellular receptor CD4. In this connection, studies on the design of new small-molecule compounds able to block the gp120-CD4 binding are still of great value. In this work, in silico design of drug-like compounds containing the moieties that make the ligand active towards gp120 was performed within the concept of click chemistry. Complexes of the designed molecules bound to gp120 were then generated by molecular docking and optimized using semiempirical quantum chemical method PM7. Finally, the binding affinity analysis of these ligand/gp120 complexes was performed by molecular dynamic simulations and binding free energy calculations. As a result, five top-ranking compounds that mimic the key interactions of CD4 with gp120 and show the high binding affinity were identified as the most promising CD4-mimemic candidates. Taken together, the data obtained suggest that these compounds may serve as promising scaffolds for the development of novel, highly potent and broad anti-HIV-1 therapeutics.
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Affiliation(s)
- Alexander M Andrianov
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, 220141 Minsk, Belarus.
| | - Grigory I Nikolaev
- United Institute of Informatics Problems, National Academy of Sciences of Belarus, 220012 Minsk, Belarus
| | - Yuri V Kornoushenko
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, 220141 Minsk, Belarus
| | - Wei Xu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, 131 Dong An Road, Fuxing Building, Shanghai 200032, China
| | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, 131 Dong An Road, Fuxing Building, Shanghai 200032, China.
| | - Alexander V Tuzikov
- United Institute of Informatics Problems, National Academy of Sciences of Belarus, 220012 Minsk, Belarus.
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Curreli F, Belov DS, Ahmed S, Ramesh RR, Kurkin AV, Altieri A, Debnath AK. Synthesis, Antiviral Activity, and Structure-Activity Relationship of 1,3-Benzodioxolyl Pyrrole-Based Entry Inhibitors Targeting the Phe43 Cavity in HIV-1 gp120. ChemMedChem 2018; 13:2332-2348. [PMID: 30257071 DOI: 10.1002/cmdc.201800534] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 09/25/2018] [Indexed: 01/30/2023]
Abstract
The pathway by which HIV-1 enters host cells is a prime target for novel drug discovery because of its critical role in the life cycle of HIV-1. The HIV-1 envelope glycoprotein gp120 plays an important role in initiating virus entry by targeting the primary cell receptor CD4. We explored the substitution of bulky molecular groups in region I in the NBD class of entry inhibitors. Previous attempts at bulky substituents in that region abolished antiviral activity, even though the binding site is hydrophobic. We synthesized a series of entry inhibitors containing the 1,3-benzodioxolyl moiety or its bioisostere, 2,1,3-benzothiadiazole. The introduction of the bulkier groups was well tolerated, and despite only minor improvements in antiviral activity, the selectivity index of these compounds improved significantly.
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Affiliation(s)
- Francesca Curreli
- Laboratory of Molecular Modeling & Drug Design, Lindsley F. Kimball Research Institute, New York Blood Center, 310 East 67th Street, New York, NY, 10065, USA
| | - Dmitry S Belov
- EDASA Scientific, Scientific Park, Moscow State University, Leninskie Gory Boulevard 75, 77-101b, 119992, Moscow, Russia
| | - Shahad Ahmed
- Laboratory of Molecular Modeling & Drug Design, Lindsley F. Kimball Research Institute, New York Blood Center, 310 East 67th Street, New York, NY, 10065, USA
| | - Ranjith R Ramesh
- Laboratory of Molecular Modeling & Drug Design, Lindsley F. Kimball Research Institute, New York Blood Center, 310 East 67th Street, New York, NY, 10065, USA
| | - Alexander V Kurkin
- EDASA Scientific, Scientific Park, Moscow State University, Leninskie Gory Boulevard 75, 77-101b, 119992, Moscow, Russia
| | - Andrea Altieri
- EDASA Scientific, Scientific Park, Moscow State University, Leninskie Gory Boulevard 75, 77-101b, 119992, Moscow, Russia
| | - Asim K Debnath
- Laboratory of Molecular Modeling & Drug Design, Lindsley F. Kimball Research Institute, New York Blood Center, 310 East 67th Street, New York, NY, 10065, USA
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Belov DS, Curreli F, Kurkin AV, Altieri A, Debnath AK. Guanidine‐Containing Phenyl‐Pyrrole Compounds as Probes for Generating HIV Entry Inhibitors Targeted to gp120. ChemistrySelect 2018. [DOI: 10.1002/slct.201801662] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Dmitry S. Belov
- EDASA Scientific Scientific ParkMoscow State University Leninskie Gory, Bld.75, 77–101b 119992 Moscow Russia
| | - Francesca Curreli
- Laboratory of Molecular Modeling and Drug DesignLindsley F. Kimball Research Institute E 67th St New York, NY 10065 USA
| | - Alexander V. Kurkin
- EDASA Scientific Scientific ParkMoscow State University Leninskie Gory, Bld.75, 77–101b 119992 Moscow Russia
| | - Andrea Altieri
- EDASA Scientific Scientific ParkMoscow State University Leninskie Gory, Bld.75, 77–101b 119992 Moscow Russia
| | - Asim K. Debnath
- Laboratory of Molecular Modeling and Drug DesignLindsley F. Kimball Research Institute E 67th St New York, NY 10065 USA
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