1
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Chagas BCA, Zhou X, Guerrero M, Ilina TV, Ishima R. Interplay between protease and reverse transcriptase dimerization in a model HIV-1 polyprotein. Protein Sci 2024; 33:e5080. [PMID: 38896002 PMCID: PMC11187873 DOI: 10.1002/pro.5080] [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: 02/12/2024] [Revised: 05/01/2024] [Accepted: 05/31/2024] [Indexed: 06/21/2024]
Abstract
The Gag-Pol polyprotein in human immunodeficiency virus type I (HIV-1) encodes enzymes that are essential for virus replication: protease (PR), reverse transcriptase (RT), and integrase (IN). The mature forms of PR, RT and IN are homodimer, heterodimer and tetramer, respectively. The precise mechanism underlying the formation of dimer or tetramer is not yet understood. Here, to gain insight into the dimerization of PR and RT in the precursor, we prepared a model precursor, PR-RT, incorporating an inactivating mutation at the PR active site, D25A, and including two residues in the p6* region, fused to a SUMO-tag, at the N-terminus of the PR region. We also prepared two mutants of PR-RT containing a dimer dissociation mutation either in the PR region, PR(T26A)-RT, or in the RT region, PR-RT(W401A). Size exclusion chromatography showed both monomer and dimer fractions in PR-RT and PR(T26A)-RT, but only monomer in PR-RT(W401A). SEC experiments of PR-RT in the presence of protease inhibitor, darunavir, significantly enhanced the dimerization. Additionally, SEC results suggest an estimated PR-RT dimer dissociation constant that is higher than that of the mature RT heterodimer, p66/p51, but slightly lower than the premature RT homodimer, p66/p66. Reverse transcriptase assays and RT maturation assays were performed as tools to assess the effects of the PR dimer-interface on these functions. Our results consistently indicate that the RT dimer-interface plays a crucial role in the dimerization in PR-RT, whereas the PR dimer-interface has a lesser role.
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Affiliation(s)
| | - Xiaohong Zhou
- Department of Structural BiologyUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
| | - Michel Guerrero
- Department of Structural BiologyUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
| | - Tatiana V. Ilina
- Department of Structural BiologyUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
| | - Rieko Ishima
- Department of Structural BiologyUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
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2
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Sankaran S, Krishnan SR, Sayed Y, Gromiha MM. Mechanism of drug resistance in HIV-1 protease subtype C in the presence of Atazanavir. Curr Res Struct Biol 2024; 7:100132. [PMID: 38435053 PMCID: PMC10907180 DOI: 10.1016/j.crstbi.2024.100132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/09/2024] [Accepted: 02/13/2024] [Indexed: 03/05/2024] Open
Abstract
AIDS is one of the deadliest diseases in the history of humankind caused by HIV. Despite the technological development, curtailing the viral infection inside human host still remains a challenge. Therapies such as HAART uses a combination of drugs to inhibit the viral activity. One of the important targets includes HIV protease and inhibiting its activity will minimize the production of mature structural proteins. However, the genetic diversity and the occurrence of drug resistant mutations adds complexity to effective drug design. In this study, we aimed at understanding the drug binding mechanism of one such subtype, namely subtype C and its insertion variant L38HL. We performed multiple molecular dynamics simulations along with binding free energy analysis of wild-type and L38HL bound to Atazanavir (ATV). From the analysis, we revealed that the insertion alters the hydrogen bond and hydrophobic interaction networks. The alterations in the interaction networks increase flexibility at the hinge-fulcrum interface. Further, the effects of these changes affect flap tip curling. Moreover, the changes in the hinge-fulcrum-cantilever interface alters the concerted motion of the functional regions leading to change in the direction of flap movement thus causing a subtle change in the active site volume. Additionally, formation of intramolecular hydrogen bonds in the ATV docked to L38HL restricted the movement of R1 and R2 groups thereby altering the interactions. Overall, the changes in the flexibility of flap together with the changes in the active site volume and compactness of the ligand provide insights for increased binding affinity of ATV with L38HL.
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Affiliation(s)
- S.V. Sankaran
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, India
| | - Sowmya R. Krishnan
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, India
| | - Yasien Sayed
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa
| | - M. Michael Gromiha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, India
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3
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Tang B, Luo S, Wang Q, Gao P, Duan L. Advanced molecular mechanisms of modified DRV compounds in targeting HIV-1 protease mutations and interrupting monomer dimerization. Phys Chem Chem Phys 2024; 26:4989-5001. [PMID: 38258432 DOI: 10.1039/d3cp05702j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
HIV-1 protease (PR) plays a crucial role in the treatment of HIV as a key target. The global issue of emerging drug resistance is escalating, and PR mutations pose a substantial challenge to the effectiveness of inhibitors. HIV-1 PR is an ideal model for studying drug resistance to inhibitors. The inhibitor, darunavir (DRV), exhibits a high genetic barrier to viral resistance, but with mutations of residues in the PR, there is also some resistance to DRV. Inhibitors can impede PR in two ways: one involves binding to the active site of the dimerization protease, and the other involves binding to the PR monomer, thereby preventing dimerization. In this study, we aimed to investigate the inhibitory effect of DRV with a modified inhibitor on PR, comparing the differences between wild-type and mutated PR, using molecular dynamics simulations. The inhibitory effect of the inhibitors on PR monomers was subsequently investigated. And molecular mechanics Poisson-Boltzmann surface area evaluated the binding free energy. The energy contribution of individual residues in the complex was accurately calculated by the alanine scanning binding interaction entropy method. The results showed that these inhibitors had strong inhibitory effects against PR mutations, with GRL-142 exhibiting potent inhibition of both the PR monomer and dimer. Improved inhibitors could strengthen hydrogen bonds and interactions with PR, thereby boosting inhibition efficacy. The binding of the inhibitor and mutation of the PR affected the distance between D25 and I50, preventing their dimerization and the development of drug resistance. This study could accelerate research targeting HIV-1 PR inhibitors and help to further facilitate drug design targeting both mechanisms.
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Affiliation(s)
- Bolin Tang
- School of Physics and Electronics, Shandogfng Normal University, Jinan, 250014, China.
| | - Song Luo
- School of Physics and Electronics, Shandogfng Normal University, Jinan, 250014, China.
| | - Qihang Wang
- School of Physics and Electronics, Shandogfng Normal University, Jinan, 250014, China.
| | - Pengfei Gao
- School of Physics and Electronics, Shandogfng Normal University, Jinan, 250014, China.
| | - Lili Duan
- School of Physics and Electronics, Shandogfng Normal University, Jinan, 250014, China.
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4
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Sepulveda GP, Gushchanskaia ES, Mora-Martin A, Esse R, Nikorich I, Ceballos A, Kwan J, Blum BC, Dholiya P, Emili A, Perissi V, Cardamone MD, Grishok A. DOT1L stimulates MYC/Mondo transcription factor activity by promoting its degradation cycle on chromatin. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.06.579191. [PMID: 38370658 PMCID: PMC10871221 DOI: 10.1101/2024.02.06.579191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
The proto-oncogene c-MYC is a key representative of the MYC transcription factor network regulating growth and metabolism. MML-1 (Myc- and Mondo-like) is its homolog in C. elegans. The functional and molecular cooperation between c-MYC and H3 lysine 79 methyltransferase DOT1L was demonstrated in several human cancer types, and we have earlier discovered the connection between C. elegans MML-1 and DOT-1.1. Here, we demonstrate the critical role of DOT1L/DOT-1.1 in regulating c-MYC/MML-1 target genes genome-wide by ensuring the removal of "spent" transcription factors from chromatin by the nuclear proteasome. Moreover, we uncover a previously unrecognized proteolytic activity of DOT1L, which may facilitate c-MYC turnover. This new mechanism of c-MYC regulation by DOT1L may lead to the development of new approaches for cancer treatment.
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Affiliation(s)
- Gian P. Sepulveda
- Department of Biochemistry & Cell Biology, Boston University School of Medicine, Boston, MA, 02118, USA
- Graduate Program in Genetics and Genomics, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Ekaterina S. Gushchanskaia
- Department of Biochemistry & Cell Biology, Boston University School of Medicine, Boston, MA, 02118, USA
- Present address: Tessera Therapeutics, Somerville, MA, 02143, USA
| | - Alexandra Mora-Martin
- Department of Biochemistry & Cell Biology, Boston University School of Medicine, Boston, MA, 02118, USA
- Present address: Spanish National Cancer Research Center (CNIO), 28029, Madrid, Spain
| | - Ruben Esse
- Department of Biochemistry & Cell Biology, Boston University School of Medicine, Boston, MA, 02118, USA
- Present address: Cell and Gene Therapy Catapult, Guy’s Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Iana Nikorich
- Department of Biochemistry & Cell Biology, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Ainhoa Ceballos
- Department of Biochemistry and Molecular Biophysics, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
- Present address: Research Unit, Diagnostica Longwood S.L. 50011 Zaragoza, Spain
| | - Julian Kwan
- Center for Network Systems Biology, Boston University, Boston, MA, 02118, USA
| | - Benjamin C. Blum
- Center for Network Systems Biology, Boston University, Boston, MA, 02118, USA
| | - Prakruti Dholiya
- Department of Biochemistry & Cell Biology, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Andrew Emili
- Department of Biochemistry & Cell Biology, Boston University School of Medicine, Boston, MA, 02118, USA
- Center for Network Systems Biology, Boston University, Boston, MA, 02118, USA
- Division of Computational Biology, Boston University School of Medicine, Boston, MA, 02118, USA
- Present address: OHSU Knight Cancer Institute, School of Medicine, Portland, OR, 97239, USA
| | - Valentina Perissi
- Department of Biochemistry & Cell Biology, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Maria D. Cardamone
- Department of Biochemistry & Cell Biology, Boston University School of Medicine, Boston, MA, 02118, USA
- Present address: Korro Bio Inc., Cambridge, MA, 02139, USA
| | - Alla Grishok
- Department of Biochemistry & Cell Biology, Boston University School of Medicine, Boston, MA, 02118, USA
- Genome Science Institute, Boston University, Boston, MA, 02118, USA
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5
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Dillenburg M, Smith J, Wagner CR. The Many Faces of Histidine Triad Nucleotide Binding Protein 1 (HINT1). ACS Pharmacol Transl Sci 2023; 6:1310-1322. [PMID: 37854629 PMCID: PMC10580397 DOI: 10.1021/acsptsci.3c00079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Indexed: 10/20/2023]
Abstract
The histidine triad nucleotide binding protein 1 (HINT1) is a nucleoside phosphoramidase that has garnered interest due to its widespread expression and participation in a broad range of biological processes. Herein, we discuss the role of HINT1 as a regulator of several CNS functions, tumor suppressor, and mast cell activator via its interactions with multiple G-protein-coupled receptors and transcription factors. Importantly, altered HINT1 expression and mutation are connected to the progression of multiple disease states, including several neuropsychiatric disorders, peripheral neuropathy, and tumorigenesis. Additionally, due to its involvement in the activation of several clinically used phosphoramidate prodrugs, tremendous efforts have been made to better understand the interactions behind nucleoside binding and phosphoramidate hydrolysis by HINT1. We detail the substrate specificity and catalytic mechanism of HINT1 hydrolysis, while highlighting the structural biology behind these efforts. The aim of this review is to summarize the multitude of biological and pharmacological functions in which HINT1 participates while addressing the areas of need for future research.
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Affiliation(s)
- Maxwell Dillenburg
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Jacob Smith
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Carston R Wagner
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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6
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Rahimi M, Taghdir M, Abasi Joozdani F. Dynamozones are the most obvious sign of the evolution of conformational dynamics in HIV-1 protease. Sci Rep 2023; 13:14179. [PMID: 37648682 PMCID: PMC10469195 DOI: 10.1038/s41598-023-40818-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 08/17/2023] [Indexed: 09/01/2023] Open
Abstract
Proteins are not static but are flexible molecules that can adopt many different conformations. The HIV-1 protease is an important target for the development of therapies to treat AIDS, due to its critical role in the viral life cycle. We investigated several dynamics studies on the HIV-1 protease families to illustrate the significance of examining the dynamic behaviors and molecular motions for an entire understanding of their dynamics-structure-function relationships. Using computer simulations and principal component analysis approaches, the dynamics data obtained revealed that: (i) The flap regions are the most obvious sign of the evolution of conformational dynamics in HIV-1 protease; (ii) There are dynamic structural regions in some proteins that contribute to the biological function and allostery of proteins via appropriate flexibility. These regions are a clear sign of the evolution of conformational dynamics of proteins, which we call dynamozones. The flap regions are one of the most important dynamozones members that are critical for HIV-1 protease function. Due to the existence of other members of dynamozones in different proteins, we propose to consider dynamozones as a footprint of the evolution of the conformational dynamics of proteins.
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Affiliation(s)
- Mohammad Rahimi
- Department of Biophysics, Faculty of Biological Science, Tarbiat Modares University, Tehran, 14115_111, Iran
| | - Majid Taghdir
- Department of Biophysics, Faculty of Biological Science, Tarbiat Modares University, Tehran, 14115_111, Iran.
| | - Farzane Abasi Joozdani
- Department of Biophysics, Faculty of Biological Science, Tarbiat Modares University, Tehran, 14115_111, Iran
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7
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Dakshinamoorthy A, Asmita A, Senapati S. Comprehending the Structure, Dynamics, and Mechanism of Action of Drug-Resistant HIV Protease. ACS OMEGA 2023; 8:9748-9763. [PMID: 36969469 PMCID: PMC10034783 DOI: 10.1021/acsomega.2c08279] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 02/23/2023] [Indexed: 06/18/2023]
Abstract
Since the emergence of the Human Immunodeficiency Virus (HIV) in the 1980s, strategies to combat HIV-AIDS are continuously evolving. Among the many tested targets to tackle this virus, its protease enzyme (PR) was proven to be an attractive option that brought about numerous research publications and ten FDA-approved drugs to inhibit the PR activity. However, the drug-induced mutations in the enzyme made these small molecule inhibitors ineffective with prolonged usage. The research on HIV PR, therefore, remains a thrust area even today. Through this review, we reiterate the importance of understanding the various structural and functional components of HIV PR in redesigning the structure-based small molecule inhibitors. We also discuss at length the currently available FDA-approved drugs and how these drug molecules induced mutations in the enzyme structure. We then recapitulate the reported mechanisms on how these drug-resistant variants remain sufficiently active to cleave the natural substrates. We end with the future scope covering the recently proposed strategies that show promise to deal with the mutations.
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8
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Deepa P, Thirumeignanam D. Understanding the impact of halogen functional group (Br, Cl, F, OH) in amprenavir ligand of the HIV protease. J Biomol Struct Dyn 2023; 41:12157-12170. [PMID: 36645135 DOI: 10.1080/07391102.2023.2166121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 01/01/2023] [Indexed: 01/17/2023]
Abstract
We focused our attention towards the most dreadful disease that threatens the mankind of 20th century - Acquired immunodeficiency syndrome (AIDS), caused through the human immunodeficiency virus (HIV) and a sexually transmitted infection (STI). In this study, our foremost interest was to identify the potency and stability of HIV ligand- Amprenavir (APV) and its modelled functional group (Br, Cl, F, CF3, CH3, NH2) ligands through halogen and hydrogen bond contact, which will have a clear portrait on the structure activity of protein ligand interactions. This will assist chemist in synthesizing novel APV ligands, which are expected to inhibit the activity of HIV-1 protease enzyme. The binding strength of Amprenavir ligand with interacting hinge region amino acid side chains: Isoleucine (ILE 147, 150, 184), Valine (VAL 82), Alanine (ALA 28), Aspartic acid (25, 30, 125, 130) and Glycine (GLY 127, 149) were understood through interaction energy calculations at HF, B3LYP, M052X, MP2 level of theories for different basis set (6-311 G**, LANL2DZ). The present work will reveal an understandable picture about the halogen and hydrogen bond interaction that grip the contact of ligand and amino acids in the hinge region. Overall the Halogen atom (Br, Cl, F) functional groups improved the binding strength of APV in HIV protease; which provide a new novel path for the functional group preference on the ligand that enclose perfectly with the amino acid in the hinge region.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Palanisamy Deepa
- Department of Physics, Manonmaniam Sundaranar University, Tirunelveli, India
| | - Duraisamy Thirumeignanam
- Department of Animal Nutrition, Veterinary College and Research Institute, Tamil Nadu Veterinary and Animal Sciences University, Tirunelveli, India
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9
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Yu YX, Wang W, Sun HB, Zhang LL, Wang LF, Yin YY. Decoding drug resistant mechanism of V32I, I50V and I84V mutations of HIV-1 protease on amprenavir binding by using molecular dynamics simulations and MM-GBSA calculations. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2022; 33:805-831. [PMID: 36322686 DOI: 10.1080/1062936x.2022.2140708] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Mutations V32I, I50V and I84V in the HIV-1 protease (PR) induce drug resistance towards drug amprenavir (APV). Multiple short molecular dynamics (MSMD) simulations and molecular mechanics generalized Born surface area (MM-GBSA) method were utilized to investigate drug-resistant mechanism of V32I, I50V and I84V towards APV. Dynamic information arising from MSMD simulations suggest that V32I, I50V and I84V highly affect structural flexibility, motion modes and conformational behaviours of two flaps in the PR. Binding free energies calculated by MM-GBSA method suggest that the decrease in binding enthalpy and the increase in binding entropy induced by mutations V32I, I50V and I84V are responsible for drug resistance of the mutated PRs on APV. The energetic contributions of separate residues on binding of APV to the PR show that V32I, I50V and I84V highly disturb the interactions of two flaps with APV and mostly drive the decrease in binding ability of APV to the PR. Thus, the conformational changes of two flaps in the PR caused by V32I, I50V and I84V play key roles in drug resistance of three mutated PR towards APV. This study can provide useful dynamics information for the design of potent inhibitors relieving drug resistance.
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Affiliation(s)
- Y X Yu
- School of Science, Shandong Jiaotong University, Jinan, China
| | - W Wang
- School of Science, Shandong Jiaotong University, Jinan, China
| | - H B Sun
- School of Science, Shandong Jiaotong University, Jinan, China
| | - L L Zhang
- School of Science, Shandong Jiaotong University, Jinan, China
| | - L F Wang
- School of Science, Shandong Jiaotong University, Jinan, China
| | - Y Y Yin
- School of Science, Shandong Jiaotong University, Jinan, China
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10
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Shabanpour Y, Sajjadi S, Behmard E, Abdolmaleki P, Keihan AH. The structural, dynamic, and thermodynamic basis of darunavir resistance of a heavily mutated HIV-1 protease using molecular dynamics simulation. Front Mol Biosci 2022; 9:927373. [PMID: 36046605 PMCID: PMC9420863 DOI: 10.3389/fmolb.2022.927373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/28/2022] [Indexed: 11/13/2022] Open
Abstract
The human immunodeficiency virus type 1 protease (HIV-1 PR) is an important enzyme in the life cycle of the HIV virus. It cleaves inactive pre-proteins of the virus and changes them into active proteins. Darunavir (DRV) suppresses the wild-type HIV-1 PR (WT-Pr) activity but cannot inhibit some mutant resistant forms (MUT-Pr). Increasing knowledge about the resistance mechanism can be helpful for designing more effective inhibitors. In this study, the mechanism of resistance of a highly MUT-Pr strain against DRV was investigated. For this purpose, complexes of DRV with WT-Pr (WT-Pr-D) and MUT-Pr (MUT-Pr-D) were studied by all-atom molecular dynamics simulation in order to extract the dynamic and energetic properties. Our data revealed that mutations increased the flap-tip flexibility due to the reduction of the flap-flap hydrophobic interactions. So, the protease’s conformation changed from a closed state to a semi-open state that can facilitate the disjunction of DRV from the active site. On the other hand, energy analysis limited to the final basins of the energy landscape indicated that the entropy of binding of DRV to MUT-Pr was more favorable than that of WT-Pr. However, the enthalpy penalty overcomes it and makes binding more unfavorable relative to the WT-Pr. The unfavorable interaction of DRV with R8, I50, I84, D25′, and A28′ residues in MUT-Pr-D relative to WT-Pr-D is the reason for this enthalpy penalty. Thus, mutations drive resistance to DRV. The hydrogen bond analysis showed that compared with WT-Pr, the hydrogen bonds between DRV and the active-site residues of MUT-Pr were disrupted.
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Affiliation(s)
- Yaser Shabanpour
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Sharareh Sajjadi
- Department of Biology, Roudehen Branch, Islamic Azad University, Roudehen, Iran
| | - Esmaeil Behmard
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Parviz Abdolmaleki
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Amir Homayoun Keihan
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
- *Correspondence: Amir Homayoun Keihan, ,
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11
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Troyano-Hernáez P, Reinosa R, Holguín A. Genetic Diversity and Low Therapeutic Impact of Variant-Specific Markers in HIV-1 Pol Proteins. Front Microbiol 2022; 13:866705. [PMID: 35910645 PMCID: PMC9330395 DOI: 10.3389/fmicb.2022.866705] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
The emergence and spread of new HIV-1 variants pose a challenge for the effectiveness of antiretrovirals (ARV) targeting Pol proteins. During viral evolution, non-synonymous mutations have fixed along the viral genome, leading to amino acid (aa) changes that can be variant-specific (V-markers). Those V-markers fixed in positions associated with drug resistance mutations (DRM), or R-markers, can impact drug susceptibility and resistance pathways. All available HIV-1 Pol sequences from ARV-naïve subjects were downloaded from the United States Los Alamos HIV Sequence Database, selecting 59,733 protease (PR), 6,437 retrotranscriptase (RT), and 6,059 integrase (IN) complete sequences ascribed to the four HIV-1 groups and group M subtypes and circulating recombinant forms (CRFs). Using a bioinformatics tool developed in our laboratory (EpiMolBio), we inferred the consensus sequences for each Pol protein and HIV-1 variant to analyze the aa conservation in Pol. We analyzed the Wu–Kabat protein variability coefficient (WK) in PR, RT, and IN group M to study the susceptibility of each site to evolutionary replacements. We identified as V-markers the variant-specific aa changes present in >75% of the sequences in variants with >5 available sequences, considering R-markers those V-markers that corresponded to DRM according to the IAS-USA2019 and Stanford-Database 9.0. The mean aa conservation of HIV-1 and group M consensus was 82.60%/93.11% in PR, 88.81%/94.07% in RT, and 90.98%/96.02% in IN. The median group M WK was 10 in PR, 4 in RT, and 5 in IN. The residues involved in binding or catalytic sites showed a variability <0.5%. We identified 106 V-markers: 31 in PR, 28 in RT, and 47 in IN, present in 11, 12, and 13 variants, respectively. Among them, eight (7.5%) were R-markers, present in five variants, being minor DRM with little potential effect on ARV susceptibility. We present a thorough analysis of Pol variability among all HIV-1 variants circulating to date. The relatively high aa conservation observed in Pol proteins across HIV-1 variants highlights their critical role in the viral cycle. However, further studies are needed to understand the V-markers’ impact on the Pol proteins structure, viral cycle, or treatment strategies, and periodic variability surveillance studies are also required to understand PR, RT, and IN evolution.
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12
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Cui Y, Taguchi A, Shida H, Konno S, Takayama K, Taniguchi A, Hayashi Y. Chemical Synthesis of an HIV-1 Protease Analog with Some Amides in a Polypeptide Main Chain Replaced by Disulfide Bonds. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2022. [DOI: 10.1246/bcsj.20220103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Yan Cui
- Department of Medicinal Chemistry, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Akihiro Taguchi
- Department of Medicinal Chemistry, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Hayate Shida
- Department of Medicinal Chemistry, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Sho Konno
- Department of Medicinal Chemistry, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Kentaro Takayama
- Department of Medicinal Chemistry, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
- Present address: Department of Environmental Biochemistry, Kyoto Pharmaceutical University, 5 Misasaginakauchi-cho, Yamashina, Kyoto 607-8414, Japan
| | - Atsuhiko Taniguchi
- Department of Medicinal Chemistry, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Yoshio Hayashi
- Department of Medicinal Chemistry, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
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13
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Wang R, Zheng Q. Multiple Molecular Dynamics Simulations and Energy Analysis Unravel the Dynamic Properties and Binding Mechanism of Mutants HIV-1 Protease with DRV and CA-p2. Microbiol Spectr 2022; 10:e0074821. [PMID: 35319278 PMCID: PMC9045218 DOI: 10.1128/spectrum.00748-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 02/10/2022] [Indexed: 11/20/2022] Open
Abstract
PRS17, a variant of human immunodeficiency virus type I protease (HIV-1 PR), has 17 mutated residues showing high levels of multidrug resistance. To describe the effects of these mutated residues on the dynamic properties and the binding mechanism of PR with substrate and inhibitor, focused on six systems (two complexes of WT PR and PRS17 with inhibitor Darunavir (DRV), two complexes of WT PR and PRS17 with substrate analogue CA-p2, two unligand WT PR and PRS17), we performed multiple molecular dynamics (MD) simulations combined with MM-PBSA and solvated interaction energy (SIE) methods. For both the unligand PRs and ligand-PR complexes, the results from simulations revealed 17 mutated residues alter the flap-flap distance, the distance from flap regions to catalytic sites, and the curling degree of the flap tips. These mutated residues changed the flexibility of the flap region in PR, and thus affected its binding energy with DRV and CA-p2, resulting in differences in sensitivity. Hydrophobic cavity makes an important contribution to the binding of PR and ligands. And most noticeable of all, the binding of the guanidine group in CA-p2 and Arg8' of PRS17 is useful for increasing their binding ability. These results have important guidance for the further design of drugs against multidrug resistant PR. IMPORTANCE Developing effective anti-HIV inhibitors is the current requirement to cope with the emergence of the resistance of mutants. Compared with the experiments, MD simulations along with energy calculations help reduce the time and cost of designing new inhibitors. Based on our simulation results, we propose two factors that may help design effective inhibitors against HIV-1 PR: (i) importance of hydrophobic cavity, and (ii) introduction of polar groups similar to the guanidine group.
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Affiliation(s)
- Ruige Wang
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, People's Republic of China
| | - Qingchuan Zheng
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, People's Republic of China
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14
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Basis for drug selectivity of plasmepsin IX and X inhibition in Plasmodium falciparum and vivax. Structure 2022; 30:947-961.e6. [PMID: 35460613 DOI: 10.1016/j.str.2022.03.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 03/02/2022] [Accepted: 03/29/2022] [Indexed: 11/20/2022]
Abstract
Plasmepsins IX (PMIX) and X (PMX) are essential aspartyl proteases for Plasmodium spp. egress, invasion, and development. WM4 and WM382 inhibit PMIX and PMX in Plasmodium falciparum and P. vivax. WM4 inhibits PMX, while WM382 is a dual inhibitor of PMIX and PMX. To understand their function, we identified protein substrates. Enzyme kinetic and structural analyses identified interactions responsible for drug specificity. PMIX and PMX have similar substrate specificity; however, there are distinct differences for peptide and protein substrates. Differences in WM4 and WM382 binding for PMIX and PMX map to variations in the S' region and engagement of the active site S3 pocket. Structures of PMX reveal interactions and mechanistic detail of drug binding important for development of clinical candidates against these targets.
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15
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Prediction and molecular field view of drug resistance in HIV-1 protease mutants. Sci Rep 2022; 12:2913. [PMID: 35190671 PMCID: PMC8861105 DOI: 10.1038/s41598-022-07012-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 02/07/2022] [Indexed: 12/04/2022] Open
Abstract
Conquering the mutational drug resistance is a great challenge in anti-HIV drug development and therapy. Quantitatively predicting the mutational drug resistance in molecular level and elucidating the three dimensional structure-resistance relationships for anti-HIV drug targets will help to improve the understanding of the drug resistance mechanism and aid the design of resistance evading inhibitors. Here the MB-QSAR (Mutation-dependent Biomacromolecular Quantitative Structure Activity Relationship) method was employed to predict the molecular drug resistance of HIV-1 protease mutants towards six drugs, and to depict the structure resistance relationships in HIV-1 protease mutants. MB-QSAR models were constructed based on a published data set of Ki values for HIV-1 protease mutants against drugs. Reliable MB-QSAR models were achieved and these models display both well internal and external prediction abilities. Interpreting the MB-QSAR models supplied structural information related to the drug resistance as well as the guidance for the design of resistance evading drugs. This work showed that MB-QSAR method can be employed to predict the resistance of HIV-1 protease caused by polymorphic mutations, which offer a fast and accurate method for the prediction of other drug target within the context of 3D structures.
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16
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Lagoutte-Renosi J, Allemand F, Ramseyer C, Yesylevskyy S, Davani S. Molecular modeling in cardiovascular pharmacology: Current state of the art and perspectives. Drug Discov Today 2021; 27:985-1007. [PMID: 34863931 DOI: 10.1016/j.drudis.2021.11.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 11/02/2021] [Accepted: 11/25/2021] [Indexed: 01/10/2023]
Abstract
Molecular modeling in pharmacology is a promising emerging tool for exploring drug interactions with cellular components. Recent advances in molecular simulations, big data analysis, and artificial intelligence (AI) have opened new opportunities for rationalizing drug interactions with their pharmacological targets. Despite the obvious utility and increasing impact of computational approaches, their development is not progressing at the same speed in different fields of pharmacology. Here, we review current in silico techniques used in cardiovascular diseases (CVDs), cardiological drug discovery, and assessment of cardiotoxicity. In silico techniques are paving the way to a new era in cardiovascular medicine, but their use somewhat lags behind that in other fields.
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Affiliation(s)
- Jennifer Lagoutte-Renosi
- EA 3920 Université Bourgogne Franche-Comté, 25000 Besançon, France; Laboratoire de Pharmacologie Clinique et Toxicologie-CHU de Besançon, 25000 Besançon, France
| | - Florentin Allemand
- EA 3920 Université Bourgogne Franche-Comté, 25000 Besançon, France; Laboratoire Chrono Environnement UMR CNRS 6249, Université de Bourgogne Franche-Comté, 16 route de Gray, 25000 Besançon, France
| | - Christophe Ramseyer
- Laboratoire Chrono Environnement UMR CNRS 6249, Université de Bourgogne Franche-Comté, 16 route de Gray, 25000 Besançon, France
| | - Semen Yesylevskyy
- Laboratoire Chrono Environnement UMR CNRS 6249, Université de Bourgogne Franche-Comté, 16 route de Gray, 25000 Besançon, France; Department of Physics of Biological Systems, Institute of Physics of The National Academy of Sciences of Ukraine, Nauky Sve. 46, Kyiv, Ukraine; Receptor.ai inc, 16192 Coastal Highway, Lewes, DE, USA
| | - Siamak Davani
- EA 3920 Université Bourgogne Franche-Comté, 25000 Besançon, France; Laboratoire de Pharmacologie Clinique et Toxicologie-CHU de Besançon, 25000 Besançon, France.
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17
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Yu YX, Liu WT, Li HY, Wang W, Sun HB, Zhang LL, Wu SL. Decoding molecular mechanism underlying binding of drugs to HIV-1 protease with molecular dynamics simulations and MM-GBSA calculations. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2021; 32:889-915. [PMID: 34551634 DOI: 10.1080/1062936x.2021.1979647] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 09/08/2021] [Indexed: 06/13/2023]
Abstract
HIV-1 protease (PR) is thought to be efficient targets of anti-AIDS drug design. Molecular dynamics (MD) simulations and multiple post-processing analysis technologies were applied to decipher molecular mechanism underlying binding of three drugs Lopinavir (LPV), Nelfinavir (NFV) and Atazanavir (ATV) to the PR. Binding free energies calculated by molecular mechanics generalized Born surface area (MM-GBSA) suggest that compensation between binding enthalpy and entropy plays a vital role in binding of drugs to PR. Dynamics analyses show that binding of LPV, NFV and ATV highly affects structural flexibility, motion modes and dynamics behaviour of the PR, especially for two flaps. Computational alanine scanning and interaction network analysis verify that although three drugs have structural difference, they share similar binding modes to the PR and common interaction clusters with the PR. The current findings also confirm that residues located interaction clusters, such as Asp25/Asp25', Gly27/Gly27', Ala28/Ala28', Asp29, Ile47/Ile47', Gly49/Gly49', Ile50/Ile50', Val82/Val82' and Ile84/Ile84, can be used as efficient targets of clinically available inhibitors towards the PR.
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Affiliation(s)
- Y X Yu
- School of Science, Shandong Jiaotong University, Jinan, China
| | - W T Liu
- Shuifa Qilu Cultural Tourism Development Co., Ltd, Shuifa Ecological Industry Group, Jinan, China
| | - H Y Li
- School of Science, Shandong Jiaotong University, Jinan, China
| | - W Wang
- School of Science, Shandong Jiaotong University, Jinan, China
| | - H B Sun
- School of Science, Shandong Jiaotong University, Jinan, China
| | - L L Zhang
- School of Science, Shandong Jiaotong University, Jinan, China
| | - S L Wu
- School of Science, Shandong Jiaotong University, Jinan, China
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18
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Sk MF, Haridev S, Roy R, Kar P. Investigating potency of TMC-126 against wild-type and mutant variants of HIV-1 protease: a molecular dynamics and free energy study. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2021; 32:941-962. [PMID: 34787532 DOI: 10.1080/1062936x.2021.1999318] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 10/25/2021] [Indexed: 06/13/2023]
Abstract
A detailed computational study was performed to investigate the conformational changes of flap region and the mechanism underlying the binding of the inhibitor TMC-126 to HIV-1 protease (PR1) and its mutant variants through molecular dynamics simulations in conjunction with the molecular mechanics Poisson-Boltzmann (MM-PBSA) free energy calculation. Further, we have studied the effectiveness of the inhibitor against HIV-2 protease (PR2). The MM-PBSA calculation suggests that TMC-126 loses its potency against mutant variants and PR2 compared to wild-type PR1 mainly due to the loss in intermolecular electrostatic interactions. The potency of the inhibitor decreases in the order: wild type PR1 > M46L > MDR20 > I50V > PR2 > V32I > A28S. Our study reveals that the flap of PR1 adopts a semi-open conformation due to the mutation I50V or MDR20. The dissimilar nature of the movement of the flap tip of both monomers is evident from the dynamic cross-correlation map. The protein structural network analysis displays that mutation causes structural rearrangements and changes the communication path between residues. Overall, we believe our study may help explore and accelerate the development of novel HIV-1/HIV-2 protease inhibitors with better potency.
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Affiliation(s)
- M F Sk
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - S Haridev
- Department of Physics, Indian Institute of Technology Indore, Indore, India
| | - R Roy
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - P Kar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
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19
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Gaber A, Pavšič M. Modeling and Structure Determination of Homo-Oligomeric Proteins: An Overview of Challenges and Current Approaches. Int J Mol Sci 2021; 22:9081. [PMID: 34445785 PMCID: PMC8396596 DOI: 10.3390/ijms22169081] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/20/2021] [Accepted: 08/20/2021] [Indexed: 12/12/2022] Open
Abstract
Protein homo-oligomerization is a very common phenomenon, and approximately half of proteins form homo-oligomeric assemblies composed of identical subunits. The vast majority of such assemblies possess internal symmetry which can be either exploited to help or poses challenges during structure determination. Moreover, aspects of symmetry are critical in the modeling of protein homo-oligomers either by docking or by homology-based approaches. Here, we first provide a brief overview of the nature of protein homo-oligomerization. Next, we describe how the symmetry of homo-oligomers is addressed by crystallographic and non-crystallographic symmetry operations, and how biologically relevant intermolecular interactions can be deciphered from the ordered array of molecules within protein crystals. Additionally, we describe the most important aspects of protein homo-oligomerization in structure determination by NMR. Finally, we give an overview of approaches aimed at modeling homo-oligomers using computational methods that specifically address their internal symmetry and allow the incorporation of other experimental data as spatial restraints to achieve higher model reliability.
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20
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Sherry D, Worth R, Sayed Y. Elasticity-Associated Functionality and Inhibition of the HIV Protease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1371:79-108. [PMID: 34351572 DOI: 10.1007/5584_2021_655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
HIV protease plays a critical role in the life cycle of the virus through the generation of mature and infectious virions. Detailed knowledge of the structure of the enzyme and its substrate has led to the development of protease inhibitors. However, the development of resistance to all currently available protease inhibitors has contributed greatly to the decreased success of antiretroviral therapy. When therapy failure occurs, multiple mutations are found within the protease sequence starting with primary mutations, which directly impact inhibitor binding, which can also negatively impact viral fitness and replicative capacity by decreasing the binding affinity of the natural substrates to the protease. As such, secondary mutations which are located outside of the active site region accumulate to compensate for the recurrently deleterious effects of primary mutations. However, the resistance mechanism of these secondary mutations is not well understood, but what is known is that these secondary mutations contribute to resistance in one of two ways, either through increasing the energetic penalty associated with bringing the protease into the closed conformation, or, through decreasing the stability of the protein/drug complex in a manner that increases the dissociation rate of the drug, leading to diminished inhibition. As a result, the elasticity of the enzyme-substrate complex has been implicated in the successful recognition and catalysis of the substrates which may be inferred to suggest that the elasticity of the enzyme/drug complex plays a role in resistance. A realistic representation of the dynamic nature of the protease may provide a more powerful tool in structure-based drug design algorithms.
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Affiliation(s)
- Dean Sherry
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa
| | - Roland Worth
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa
| | - Yasien Sayed
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa.
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21
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Yu YX, Wang W, Sun HB, Zhang LL, Wu SL, Liu WT. Insights into effect of the Asp25/Asp25' protonation states on binding of inhibitors Amprenavir and MKP97 to HIV-1 protease using molecular dynamics simulations and MM-GBSA calculations. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2021; 32:615-641. [PMID: 34157882 DOI: 10.1080/1062936x.2021.1939149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 06/02/2021] [Indexed: 06/13/2023]
Abstract
The protonation states of two aspartic acids in the catalytic strands of HIV-1 protease (PR) remarkably affect bindings of inhibitors to PR. It is requisite for the design of potent inhibitors towards PR to investigate the influences of Asp25/Asp25' protonated states on dynamics behaviour of PR and binding mechanism of inhibitors to PR. In this work, molecular dynamics (MD) simulations, MM-GBSA method and principal component (PC) analysis were coupled to explore the effect of Asp25/Asp25' protonation states on conformational changes of PR and bindings of Amprenavir and MKP97 to PR. The results show that the Asp25/Asp25' protonation states exert different impacts on structural fluctuations, flexibility and motion modes of PR. Dynamics analysis verifies that Asp25/Asp25' protonated states highly affect conformational dynamics of two flaps in PR. The binding free energy calculations results suggest that the Asp25/Asp25' protonated states obviously strengthen bindings of inhibitors to PR compared to the non-protonation state. Calculations of residue-based free energy decomposition indicate that the Asp25/Asp25' protonation not only disturbs the interaction network of inhibitors with PR but also stabilizes bindings of inhibitors to PR by cancelling the electrostatic repulsive interaction. Therefore, special attentions should be paid to the Asp25/Asp25' protonation in the design of potent inhibitors towards PR.
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Affiliation(s)
- Y X Yu
- School of Science, Shandong Jiaotong University, Jinan, China
| | - W Wang
- School of Science, Shandong Jiaotong University, Jinan, China
| | - H B Sun
- School of Science, Shandong Jiaotong University, Jinan, China
| | - L L Zhang
- School of Science, Shandong Jiaotong University, Jinan, China
| | - S L Wu
- School of Science, Shandong Jiaotong University, Jinan, China
| | - W T Liu
- School of Science, Shandong Jiaotong University, Jinan, China
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22
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Kryštůfek R, Šácha P, Starková J, Brynda J, Hradilek M, Tloušt'ová E, Grzymska J, Rut W, Boucher MJ, Drąg M, Majer P, Hájek M, Řezáčová P, Madhani HD, Craik CS, Konvalinka J. Re-emerging Aspartic Protease Targets: Examining Cryptococcus neoformans Major Aspartyl Peptidase 1 as a Target for Antifungal Drug Discovery. J Med Chem 2021; 64:6706-6719. [PMID: 34006103 PMCID: PMC8165695 DOI: 10.1021/acs.jmedchem.0c02177] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Cryptococcosis is
an invasive infection that accounts for 15% of
AIDS-related fatalities. Still, treating cryptococcosis remains a
significant challenge due to the poor availability of effective antifungal
therapies and emergence of drug resistance. Interestingly, protease
inhibitor components of antiretroviral therapy regimens have shown
some clinical benefits in these opportunistic infections. We investigated
Major aspartyl peptidase 1 (May1), a secreted Cryptococcus
neoformans protease, as a possible target for the
development of drugs that act against both fungal and retroviral aspartyl
proteases. Here, we describe the biochemical characterization of May1,
present its high-resolution X-ray structure, and provide its substrate
specificity analysis. Through combinatorial screening of 11,520 compounds,
we identified a potent inhibitor of May1 and HIV protease. This dual-specificity
inhibitor exhibits antifungal activity in yeast culture, low cytotoxicity,
and low off-target activity against host proteases and could thus
serve as a lead compound for further development of May1 and HIV protease
inhibitors.
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Affiliation(s)
- Robin Kryštůfek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo n. 2, Prague 6 16610, Czech Republic.,Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles UniversityHlavova 8, Prague 2 12843, Czech Republic
| | - Pavel Šácha
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo n. 2, Prague 6 16610, Czech Republic.,Department of Biochemistry, Faculty of Science, Charles UniversityHlavova 8, Prague 2 12843, Czech Republic
| | - Jana Starková
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo n. 2, Prague 6 16610, Czech Republic
| | - Jiří Brynda
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo n. 2, Prague 6 16610, Czech Republic.,Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, Prague 4 14220, Czech Republic
| | - Martin Hradilek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo n. 2, Prague 6 16610, Czech Republic
| | - Eva Tloušt'ová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo n. 2, Prague 6 16610, Czech Republic
| | - Justyna Grzymska
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, Wroclaw 50-370, Poland
| | - Wioletta Rut
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, Wroclaw 50-370, Poland
| | - Michael J Boucher
- Department of Biochemistry & Biophysics, University of California, San Francisco, UCSF Genentech Hall, 600 16th St Rm N374, San Francisco, California 94158, United States
| | - Marcin Drąg
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, Wroclaw 50-370, Poland
| | - Pavel Majer
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo n. 2, Prague 6 16610, Czech Republic
| | - Miroslav Hájek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo n. 2, Prague 6 16610, Czech Republic
| | - Pavlína Řezáčová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo n. 2, Prague 6 16610, Czech Republic.,Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, Prague 4 14220, Czech Republic
| | - Hiten D Madhani
- Department of Biochemistry & Biophysics, University of California, San Francisco, UCSF Genentech Hall, 600 16th St Rm N374, San Francisco, California 94158, United States.,Chan-Zuckerberg Biohub, 499 Illinois Street, San Francisco, California 94158, United States
| | - Charles S Craik
- Department of Pharmaceutical Chemistry, University of California San Francisco, UCSF Genentech Hall, 600 16th St Rm S512, San Francisco, California 94158, United States
| | - Jan Konvalinka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo n. 2, Prague 6 16610, Czech Republic.,Department of Biochemistry, Faculty of Science, Charles UniversityHlavova 8, Prague 2 12843, Czech Republic
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23
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Advancements in macromolecular crystallography: from past to present. Emerg Top Life Sci 2021; 5:127-149. [PMID: 33969867 DOI: 10.1042/etls20200316] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 04/09/2021] [Accepted: 04/15/2021] [Indexed: 11/17/2022]
Abstract
Protein Crystallography or Macromolecular Crystallography (MX) started as a new discipline of science with the pioneering work on the determination of the protein crystal structures by John Kendrew in 1958 and Max Perutz in 1960. The incredible achievements in MX are attributed to the development of advanced tools, methodologies, and automation in every aspect of the structure determination process, which have reduced the time required for solving protein structures from years to a few days, as evident from the tens of thousands of crystal structures of macromolecules available in PDB. The advent of brilliant synchrotron sources, fast detectors, and novel sample delivery methods has shifted the paradigm from static structures to understanding the dynamic picture of macromolecules; further propelled by X-ray Free Electron Lasers (XFELs) that explore the femtosecond regime. The revival of the Laue diffraction has also enabled the understanding of macromolecules through time-resolved crystallography. In this review, we present some of the astonishing method-related and technological advancements that have contributed to the progress of MX. Even with the rapid evolution of several methods for structure determination, the developments in MX will keep this technique relevant and it will continue to play a pivotal role in gaining unprecedented atomic-level details as well as revealing the dynamics of biological macromolecules. With many exciting developments awaiting in the upcoming years, MX has the potential to contribute significantly to the growth of modern biology by unraveling the mechanisms of complex biological processes as well as impacting the area of drug designing.
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24
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Weber IT, Wang YF, Harrison RW. HIV Protease: Historical Perspective and Current Research. Viruses 2021; 13:v13050839. [PMID: 34066370 PMCID: PMC8148205 DOI: 10.3390/v13050839] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/01/2021] [Accepted: 05/03/2021] [Indexed: 12/15/2022] Open
Abstract
The retroviral protease of human immunodeficiency virus (HIV) is an excellent target for antiviral inhibitors for treating HIV/AIDS. Despite the efficacy of therapy, current efforts to control the disease are undermined by the growing threat posed by drug resistance. This review covers the historical background of studies on the structure and function of HIV protease, the subsequent development of antiviral inhibitors, and recent studies on drug-resistant protease variants. We highlight the important contributions of Dr. Stephen Oroszlan to fundamental knowledge about the function of the HIV protease and other retroviral proteases. These studies, along with those of his colleagues, laid the foundations for the design of clinical inhibitors of HIV protease. The drug-resistant protease variants also provide an excellent model for investigating the molecular mechanisms and evolution of resistance.
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Affiliation(s)
- Irene T. Weber
- Department of Biology, Georgia State University, Atlanta, GA 30302, USA;
- Correspondence:
| | - Yuan-Fang Wang
- Department of Biology, Georgia State University, Atlanta, GA 30302, USA;
| | - Robert W. Harrison
- Department of Computer Science, Georgia State University, Atlanta, GA 30302, USA;
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25
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Mangiagalli M, Barbiroli A, Santambrogio C, Ferrari C, Nardini M, Lotti M, Brocca S. The activity and stability of a cold-active acylaminoacyl peptidase rely on its dimerization by domain swapping. Int J Biol Macromol 2021; 181:263-274. [PMID: 33775759 DOI: 10.1016/j.ijbiomac.2021.03.150] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/15/2021] [Accepted: 03/23/2021] [Indexed: 01/07/2023]
Abstract
The study of enzymes from extremophiles arouses interest in Protein Science because of the amazing solutions these proteins adopt to cope with extreme conditions. Recently solved, the structure of the psychrophilic acyl aminoacyl peptidase from Sporosarcina psychrophila (SpAAP) pinpoints a mechanism of dimerization unusual for this class of enzymes. The quaternary structure of SpAAP relies on a domain-swapping mechanism involving the N-terminal A1 helix. The A1 helix is conserved among homologous mesophilic and psychrophilic proteins and its deletion causes the formation of a monomeric enzyme, which is inactive and prone to aggregate. Here, we investigate the dimerization mechanism of SpAAP through the analysis of chimeric heterodimers where a protomer lacking the A1 helix combines with a protomer carrying the inactivated catalytic site. Our results indicate that the two active sites are independent, and that a single A1 helix is sufficient to partially recover the quaternary structure and the activity of chimeric heterodimers. Since catalytically competent protomers are unstable and inactive unless they dimerize, SpAAP reveals as an "obligomer" for both structural and functional reasons.
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Affiliation(s)
- Marco Mangiagalli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy.
| | - Alberto Barbiroli
- Department of Food, Environmental and Nutritional Sciences, University of Milano, Via Celoria 2, 20133 Milano, Italy
| | - Carlo Santambrogio
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Cristian Ferrari
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Marco Nardini
- Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milano, Italy
| | - Marina Lotti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Stefania Brocca
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy.
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Prioritizing antiviral drugs against SARS-CoV-2 by integrating viral complete genome sequences and drug chemical structures. Sci Rep 2021; 11:6248. [PMID: 33737523 PMCID: PMC7973547 DOI: 10.1038/s41598-021-83737-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 12/18/2020] [Indexed: 12/21/2022] Open
Abstract
The outbreak of a novel febrile respiratory disease called COVID-19, caused by a newfound coronavirus SARS-CoV-2, has brought a worldwide attention. Prioritizing approved drugs is critical for quick clinical trials against COVID-19. In this study, we first manually curated three Virus-Drug Association (VDA) datasets. By incorporating VDAs with the similarity between drugs and that between viruses, we constructed a heterogeneous Virus-Drug network. A novel Random Walk with Restart method (VDA-RWR) was then developed to identify possible VDAs related to SARS-CoV-2. We compared VDA-RWR with three state-of-the-art association prediction models based on fivefold cross-validations (CVs) on viruses, drugs and virus-drug associations on three datasets. VDA-RWR obtained the best AUCs for the three fivefold CVs, significantly outperforming other methods. We found two small molecules coming together on the three datasets, that is, remdesivir and ribavirin. These two chemical agents have higher molecular binding energies of − 7.0 kcal/mol and − 6.59 kcal/mol with the domain bound structure of the human receptor angiotensin converting enzyme 2 (ACE2) and the SARS-CoV-2 spike protein, respectively. Interestingly, for the first time, experimental results suggested that navitoclax could be potentially applied to stop SARS-CoV-2 and remains to further validation.
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Malki Y, Martinez J, Masurier N. 1,3-Diazepine: A privileged scaffold in medicinal chemistry. Med Res Rev 2021; 41:2247-2315. [PMID: 33645848 DOI: 10.1002/med.21795] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 01/20/2021] [Accepted: 02/17/2021] [Indexed: 12/19/2022]
Abstract
Privileged structures have been widely used as effective templates for drug discovery. While benzo-1,4-diazepine constitutes the first historical example of such a structure, the 1,3 analogue is just as rich in terms of applications in medicinal chemistry. The 1,3-diazepine moiety is present in numerous biological active compounds including natural products, and is used to design compounds displaying a large range of biological activities. It is present in the clinically used anticancer compound pentostatin, in several recent FDA approved β-lactamase inhibitors (e.g., avibactam) and also in coformycin, a natural product known as a ring-expanded purine analogue displaying antiviral and anticancer activities. Several other 1,3-diazepine containing compounds have entered into clinical trials. This heterocyclic structure has been and is still widely used in medicinal chemistry to design enzyme inhibitors, GPCR ligands, and so forth. This review endeavours to highlight the main use of the 1,3-diazepine scaffold and its derivatives, and their applications in medicinal chemistry, drug design, and therapy. We will focus more particularly on the development of enzyme inhibitors incorporating this scaffold, with a strong emphasis on the molecular interactions involved in the inhibition mechanism.
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Affiliation(s)
- Yohan Malki
- IBMM, Université de Montpellier, CNRS, ENSCM, Montpellier, France
| | - Jean Martinez
- IBMM, Université de Montpellier, CNRS, ENSCM, Montpellier, France
| | - Nicolas Masurier
- IBMM, Université de Montpellier, CNRS, ENSCM, Montpellier, France
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28
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Wang R, Zheng Q. Multiple Molecular Dynamics Simulations of the Inhibitor GRL-02031 Complex with Wild Type and Mutant HIV-1 Protease Reveal the Binding and Drug-Resistance Mechanism. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:13817-13832. [PMID: 33175558 DOI: 10.1021/acs.langmuir.0c02151] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Human immunodeficiency virus type 1 (HIV-1) protease is regarded as a fascinating target for drug development against HIV infection. However, mutations causing drug resistance severely limit the efficiency of the recently marketed drugs in the treatment of HIV replication. To elucidate the binding mechanism of HIV-1 protease with promising inhibitor GRL-02031 and further to probe the resistance mechanism associated with mutations (I47V, L76V, V82A, and N88D) to the inhibitor, we applied multiple molecular dynamics (MMD) simulations along with energy analysis by the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) and solvated interaction energy (SIE) methodology on specific HIV-1 protease with GRL-0231 complexes. On the basis of detail analysis of the simulations, we revealed key characteristics that constitute the drug resistance of four mutation HIV-1 proteases toward GRL-02031: substitution of the side chain in these four mutation residues leads to a change in the distances between the flaps and catalytic sites, thereby reducing the affinity for GRL-02031 with these four mutation proteases, even though the L76V and N88D residues cannot directly contact GRL-02031. The results of energy analysis according to the MM-PBSA and SIE methods further indicated that hydrophobic interaction was considered to be the prime driving force for inhibitor GRL-02031 binding to protease and the decrease in van der Waals interactions between inhibitor GRL-02031 and mutant proteases as the primary cause of the drug resistance. Analyses of the hydrogen bonds and atomic interactions further provided detailed explanations for the resistance of these four mutation proteases toward inhibitor GRL-02031. The present study provides potential guidance on the structure-based inhibitors' design targeting HIV-1 protease.
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Affiliation(s)
- Ruige Wang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, P. R. China
| | - Qingchuan Zheng
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, P. R. China
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, College of Life Science, Jilin University, Changchun 130023, People's Republic of China
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29
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Sanusi ZK, Lawal MM, Gupta PL, Govender T, Baijnath S, Naicker T, Maguire GEM, Honarparvar B, Roitberg AE, Kruger HG. Exploring the concerted mechanistic pathway for HIV-1 PR-substrate revealed by umbrella sampling simulation. J Biomol Struct Dyn 2020; 40:1736-1747. [PMID: 33073714 DOI: 10.1080/07391102.2020.1832578] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
HIV-1 protease (HIV-1 PR) is an essential enzyme for the replication process of its virus, and therefore considered an important target for the development of drugs against the acquired immunodeficiency syndrome (AIDS). Our previous study shows that the catalytic mechanism of subtype B/C-SA HIV-1 PR follows a one-step concerted acyclic hydrolysis reaction process using a two-layered ONIOM B3LYP/6-31++G(d,p) method. This present work is aimed at exploring the proposed mechanism of the proteolysis catalyzed by HIV-1 PR and to ensure our proposed mechanism is not an artefact of a single theoretical technique. Hence, we present umbrella sampling method that is suitable for calculating potential mean force (PMF) for non-covalent ligand/substrate-enzyme association/dissociation interactions which provide thermodynamic details for molecular recognition. The free activation energy results were computed in terms of PMF analysis within the hybrid QM(DFTB)/MM approach. The theoretical findings suggest that the proposed mechanism corresponds in principle with experimental data. Given our observations, we suggest that the QM/MM MD method can be used as a reliable computational technique to rationalize lead compounds against specific targets such as the HIV-1 protease.
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Affiliation(s)
- Zainab K Sanusi
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Monsurat M Lawal
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Pancham Lal Gupta
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | | | - Sooraj Baijnath
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Tricia Naicker
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Glenn E M Maguire
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.,School of Chemistry and Physics, University of KwaZulu-Natal, Durban, South Africa
| | - Bahareh Honarparvar
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Adrian E Roitberg
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | - Hendrik G Kruger
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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30
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Dogan B, Durdagi S. Drug Re-positioning Studies for Novel HIV-1 Inhibitors Using Binary QSAR Models and Multi-target-driven In Silico Studies. Mol Inform 2020; 40:e2000012. [PMID: 33405326 DOI: 10.1002/minf.202000012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 08/16/2020] [Indexed: 12/20/2022]
Abstract
Current antiretroviral therapies against HIV involve the usage of at least two drugs that target different stages of HIV life cycle. However, potential drug interactions and side effects pose a problem. A promising concept for complex disease treatment is 'one molecule-multiple target' approach to overcome undesired effects of multiple drugs. Additionally, it is beneficial to consider drug re-purposing due to the cost of taking a drug into the market. Taking these into account, here potential anti-HIV compounds are suggested by virtually screening small approved drug molecules and clinical candidates. Initially, binary QSAR models are used to predict the therapeutic activity of around 7900 compounds against HIV and to predict the toxicity of molecules with high therapeutic activities. Selected compounds are considered for molecular docking studies against two targets, HIV-1 protease enzyme, and chemokine co-receptor CCR5. The top docking poses for all 549 molecules are then subjected to short (1 ns) individual molecular dynamics (MD) simulations and they are ranked based on their calculated relative binding free energies. Finally, 25 molecules are selected for long (200 ns) MD simulations, and 5 molecules are suggested as promising multi-target HIV agents. The results of this study may open new avenues for the designing of new dual HIV-1 inhibitor scaffolds.
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Affiliation(s)
- Berna Dogan
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
| | - Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
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31
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Peptidyl Fluoromethyl Ketones and Their Applications in Medicinal Chemistry. Molecules 2020; 25:molecules25174031. [PMID: 32899354 PMCID: PMC7504820 DOI: 10.3390/molecules25174031] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/31/2020] [Accepted: 09/01/2020] [Indexed: 12/29/2022] Open
Abstract
Peptidyl fluoromethyl ketones occupy a pivotal role in the current scenario of synthetic chemistry, thanks to their numerous applications as inhibitors of hydrolytic enzymes. The insertion of one or more fluorine atoms adjacent to a C-terminal ketone moiety greatly modifies the physicochemical properties of the overall substrate, especially by increasing the reactivity of this functionalized carbonyl group toward nucleophiles. The main application of these peptidyl α-fluorinated ketones in medicinal chemistry relies in their ability to strongly and selectively inhibit serine and cysteine proteases. These compounds can be used as probes to study the proteolytic activity of the aforementioned proteases and to elucidate their role in the insurgence and progress on several diseases. Likewise, if the fluorinated methyl ketone moiety is suitably connected to a peptidic backbone, it may confer to the resulting structure an excellent substrate peculiarity and the possibility of being recognized by a specific subclass of human or pathogenic proteases. Therefore, peptidyl fluoromethyl ketones are also currently highly exploited for the target-based design of compounds for the treatment of topical diseases such as various types of cancer and viral infections.
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32
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A Personal History of Using Crystals and Crystallography to Understand Biology and Advanced Drug Discovery. CRYSTALS 2020. [DOI: 10.3390/cryst10080676] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Over the past 60 years, the use of crystals to define structures of complexes using X-ray analysis has contributed to the discovery of new medicines in a very significant way. This has been in understanding not only small-molecule inhibitors of proteins, such as enzymes, but also protein or peptide hormones or growth factors that bind to cell surface receptors. Experimental structures from crystallography have also been exploited in software to allow prediction of structures of important targets based on knowledge of homologues. Crystals and crystallography continue to contribute to drug design and provide a successful example of academia–industry collaboration.
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33
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Sensing HIV Protease and Its Inhibitor Using "Helical Epitope"-Imprinted Polymers. SENSORS 2020; 20:s20123592. [PMID: 32630459 PMCID: PMC7348739 DOI: 10.3390/s20123592] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 06/21/2020] [Accepted: 06/22/2020] [Indexed: 12/15/2022]
Abstract
A helical epitope-peptide (lle85-Gly94) was selected from the α-helix structure of the HIV protease (PR) as the template, which represents an intricate interplay between structure conformation and dimerization. The peptide template was mixed with water, trifluoroethanol (TFE), and acetonitrile (ACN) at a certain ratio to enlarge the helical conformation in the solution for the fabrication of helical epitope-mediated molecularly imprinted polymers (HEMIPs) on a quartz crystal microbalance (QCM) chip. The template molecules were then removed under equilibrium batch rebinding conditions involving 5% acetic acid/water. The resulting HEMIPs chip exhibited a high affinity toward template peptide HIV PR85-94, His-tagged HIV PR, and HIV PR, with dissociation constants (Kd) as 160, 43.3, and 78.5 pM, respectively. The detection limit of the developed HIV PR85-94 QCM sensor is 0.1 ng/mL. The HEMIPs chip exhibited a high affinity and selectivity to bind HIV PR and subsequently to an inhibitor of HIV PR (nelfinavir). The HIV PR binding site was properly oriented on the HEMIPs-chip to develop a HIV PR/HEMIPs chip, which can effectively bind nelfinavir to establish a sandwich assay. The nelfinavir then attached to the HIV PR/HEMIPs chip, which can be easily removed involving 0.8% acetic acid/water. Therefore, HIV PR/HEMIPs chip can be useful to screen for other HIV PR inhibitors. This technique may improve drug targeting for HIV therapy and also strengthen investigations into other virus assays.
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Kumar M, Mandal K, Blakeley MP, Wymore T, Kent SBH, Louis JM, Das A, Kovalevsky A. Visualizing Tetrahedral Oxyanion Bound in HIV-1 Protease Using Neutrons: Implications for the Catalytic Mechanism and Drug Design. ACS OMEGA 2020; 5:11605-11617. [PMID: 32478251 PMCID: PMC7254801 DOI: 10.1021/acsomega.0c00835] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 04/30/2020] [Indexed: 06/11/2023]
Abstract
HIV-1 protease is indispensable for virus propagation and an important therapeutic target for antiviral inhibitors to treat AIDS. As such inhibitors are transition-state mimics, a detailed understanding of the enzyme mechanism is crucial for the development of better anti-HIV drugs. Here, we used room-temperature joint X-ray/neutron crystallography to directly visualize hydrogen atoms and map hydrogen bonding interactions in a protease complex with peptidomimetic inhibitor KVS-1 containing a reactive nonhydrolyzable ketomethylene isostere, which, upon reacting with the catalytic water molecule, is converted into a tetrahedral intermediate state, KVS-1TI. We unambiguously determined that the resulting tetrahedral intermediate is an oxyanion, rather than the gem-diol, and both catalytic aspartic acid residues are protonated. The oxyanion tetrahedral intermediate appears to be unstable, even though the negative charge on the oxyanion is delocalized through a strong n → π* hyperconjugative interaction into the nearby peptidic carbonyl group of the inhibitor. To better understand the influence of the ketomethylene isostere as a protease inhibitor, we have also examined the protease structure and binding affinity with keto-darunavir (keto-DRV), which similar to KVS-1 includes the ketomethylene isostere. We show that keto-DRV is a significantly less potent protease inhibitor than DRV. These findings shed light on the reaction mechanism of peptide hydrolysis catalyzed by HIV-1 protease and provide valuable insights into further improvements in the design of protease inhibitors.
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Affiliation(s)
- Mukesh Kumar
- Protein Crystallography
Section, Radiation Biology and Health Sciences Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, India
| | - Kalyaneswar Mandal
- Departments of Chemistry, and Biochemistry and Molecular Biology,
Institute for Biophysical Dynamics, University
of Chicago, Chicago, Illinois 60637, United States
| | - Matthew P. Blakeley
- Large Scale Structures Group, Institut Laue−Langevin, 38000 Grenoble, France
| | - Troy Wymore
- Department of Chemistry, University
of Michigan, Ann Arbor, Michigan 48109, United States
| | - Stephen B. H. Kent
- Departments of Chemistry, and Biochemistry and Molecular Biology,
Institute for Biophysical Dynamics, University
of Chicago, Chicago, Illinois 60637, United States
| | - John M. Louis
- Laboratory of Chemical Physics, National
Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, Maryland 20892-0520, United States
| | - Amit Das
- Protein Crystallography
Section, Radiation Biology and Health Sciences Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, India
| | - Andrey Kovalevsky
- Neutron Scattering
Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
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35
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Novel radial distribution function approach in the study of point mutations: the HIV-1 protease case study. Future Med Chem 2020; 12:1025-1036. [PMID: 32319305 DOI: 10.4155/fmc-2020-0042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background: Mutations are one of the engines of evolution. Under constant stress pressure, mutations can lead to the emergence of unwanted, drug-resistant entities. Methodology: The radial distribution function weighted by the number of valence shell electrons is used to design quantitative structure-activity relationship (QSAR) model relating descriptors with the inhibition constant for a series of wild-type HIV-1 protease inhibitor complexes. The residuals of complexes with mutant HIV-1 protease were correlated with the energy of the highest occupied molecular orbitals of the residues introduced to enzyme via point mutations. Conclusion: Successful identification of residues Ile3, Asp25, Val32 and Ile50 as the one whose substitution influences the inhibition constant the most, demonstrates the potential of the proposed methodology for the study of the effects of point mutations.
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36
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Inhibition of the activity of HIV-1 protease through antibody binding and mutations probed by molecular dynamics simulations. Sci Rep 2020; 10:5501. [PMID: 32218488 PMCID: PMC7098958 DOI: 10.1038/s41598-020-62423-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 03/12/2020] [Indexed: 01/31/2023] Open
Abstract
HIV-1 protease is an essential enzyme in the life cycle of the HIV-1 virus. The conformational dynamics of the flap region of the protease is critical for the ligand binding mechanism, as well as for the catalytic activity. The monoclonal antibody F11.2.32 raised against HIV-1 protease inhibits its activity on binding. We have studied the conformational dynamics of protease in its free, inhibitor ritonavir and antibody bound forms using molecular dynamics simulations. We find that upon Ab binding to the epitope region (residues 36-46) of protease, the overall flexibility of the protease is decreased including the flap region and the active site, which is similar to the decrease in flexibility observed by inhibitor binding to the protease. This suggests an allosteric mechanism to inhibit protease activity. Further, the protease mutants G40E and G40R are known to have decreased activity and were also subjected to MD simulations. We find that the loss of flexibility in the mutants is similar to that observed in the protease bound to the Ab/inhibitor. These insights highlight the role played by dynamics in the function of the protease and how control of flexibility through Ab binding and site specific mutations can inhibit protease activity.
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37
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Abstract
The advent of the X-ray free electron laser (XFEL) in the last decade created the discipline of serial crystallography but also the challenge of how crystal samples are delivered to X-ray. Early sample delivery methods demonstrated the proof-of-concept for serial crystallography and XFEL but were beset with challenges of high sample consumption, jet clogging and low data collection efficiency. The potential of XFEL and serial crystallography as the next frontier of structural solution by X-ray for small and weakly diffracting crystals and provision of ultra-fast time-resolved structural data spawned a huge amount of scientific interest and innovation. To utilize the full potential of XFEL and broaden its applicability to a larger variety of biological samples, researchers are challenged to develop better sample delivery methods. Thus, sample delivery is one of the key areas of research and development in the serial crystallography scientific community. Sample delivery currently falls into three main systems: jet-based methods, fixed-target chips, and drop-on-demand. Huge strides have since been made in reducing sample consumption and improving data collection efficiency, thus enabling the use of XFEL for many biological systems to provide high-resolution, radiation damage-free structural data as well as time-resolved dynamics studies. This review summarizes the current main strategies in sample delivery and their respective pros and cons, as well as some future direction.
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38
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Haas DJ. The early history of cryo-cooling for macromolecular crystallography. IUCRJ 2020; 7:148-157. [PMID: 32148843 PMCID: PMC7055388 DOI: 10.1107/s2052252519016993] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 12/19/2019] [Indexed: 06/10/2023]
Abstract
This paper recounts the first successful cryo-cooling of protein crystals that demonstrated the reduction in X-ray damage to macromolecular crystals. The project was suggested by David C. Phillips in 1965 at the Royal Institution of Great Britain and continued in 1967 at the Weizmann Institute of Science, where the first cryo-cooling experiments were performed on lysozyme crystals, and was completed in 1969 at Purdue University on lactate dehydrogenase crystals. A 1970 publication in Acta Crystallographica described the cryo-procedures, the use of cryo-protectants to prevent ice formation, the importance of fast, isotropic cryo-cooling and the collection of analytical data showing more than a tenfold decrease in radiation damage in cryo-cooled lactate dehydrogenase crystals. This was the first demonstration of any method that reduced radiation damage in protein crystals, which provided crystallographers with suitable means to employ synchrotron X-ray sources for protein-crystal analysis. Today, fifty years later, more than 90% of the crystal structures deposited in the Protein Data Bank have been cryo-cooled.
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Affiliation(s)
- David J. Haas
- Tecco Corporation, 19 West Gate Road, Suffern, NY 10901, USA
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39
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Sk MF, Roy R, Kar P. Exploring the potency of currently used drugs against HIV-1 protease of subtype D variant by using multiscale simulations. J Biomol Struct Dyn 2020; 39:988-1003. [PMID: 32000612 DOI: 10.1080/07391102.2020.1724196] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Acquired immune deficiency syndrome (AIDS) is caused by the human immunodeficiency virus (HIV), type 1 and 2. Further, the diversity in HIV-1 has given rise to many serotypes and recombinant strains. The currently used protease inhibitors have been developed for subtype B, although non-B subtype strains account for ∼ 90% of the global HIV infections. Subtype D is spreading rapidly and infecting a large population in North Africa and the Middle East. In the current study, molecular dynamics simulations in conjunction with the molecular mechanics/Poisson-Boltzmann surface area (MM-PBSA) scheme was used to investigate the potency of four drugs, namely atazanavir (ATV), darunavir (DRV), lopinavir (LPV) and tipranavir (TPV) against the subtype D variant. Our calculations predicted that the potency of the inhibitors decreased in the order TPV > ATV > DRV > LPV. TPV was found to be the most potent against subtype D due to an increase in van der Waals and electrostatic interactions and reduction in the desolvation energy compared to other inhibitors. This result is further supported by the hydrogen bond interactions between inhibitors and protease. Furthermore, our analyses suggested that the binding of TPV induced a more closed conformation of the flap compared to apo or other complexes. It was observed that TPV/PRD has a lower cavity volume relative to the other three complexes leading to a tighter binding. The open conformation of the flap was observed for LPV/PRD. We expect that this study might be useful for designing more potent inhibitors against HIV-1 subtype D. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Md Fulbabu Sk
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol Campus, Indore, Madhya Pradesh, India
| | - Rajarshi Roy
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol Campus, Indore, Madhya Pradesh, India
| | - Parimal Kar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol Campus, Indore, Madhya Pradesh, India
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40
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Mahasenan KV, Batuecas MT, De Benedetti S, Kim C, Rana N, Lee M, Hesek D, Fisher JF, Sanz-Aparicio J, Hermoso JA, Mobashery S. Catalytic Cycle of Glycoside Hydrolase BglX from Pseudomonas aeruginosa and Its Implications for Biofilm Formation. ACS Chem Biol 2020; 15:189-196. [PMID: 31877028 PMCID: PMC7995829 DOI: 10.1021/acschembio.9b00754] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
BglX is a heretofore uncharacterized periplasmic glycoside hydrolase (GH) of the human pathogen Pseudomonas aeruginosa. X-ray analysis identifies it as a protein homodimer. The two active sites of the homodimer comprise catalytic residues provided by each monomer. This arrangement is seen in <2% of the hydrolases of known structure. In vitro substrate profiling shows BglX is a catalyst for β-(1→2) and β-(1→3) saccharide hydrolysis. Saccharides with β-(1→4) or β-(1→6) bonds, and the β-(1→4) muropeptides from the cell-wall peptidoglycan, are not substrates. Additional structural insights from X-ray analysis (including structures of a mutant enzyme-derived Michaelis complex, two transition-state mimetics, and two enzyme-product complexes) enabled the comprehensive description of BglX catalysis. The half-chair (4H3) conformation of the transition-state oxocarbenium species, the approach of the hydrolytic water molecule to the oxocarbenium species, and the stepwise release of the two reaction products were also visualized. The substrate pattern for BglX aligns with the [β-(1→2)-Glc]x and [β-(1→3)-Glc]x periplasmic osmoregulated periplasmic glucans, and possibly with the Psl exopolysaccharides, of P. aeruginosa. Both polysaccharides are implicated in biofilm formation. Accordingly, we show that inactivation of the bglX gene of P. aeruginosa PAO1 attenuates biofilm formation.
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Affiliation(s)
- Kiran V Mahasenan
- Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , Indiana 46556 , United States
| | - María T Batuecas
- Department of Crystallography and Structural Biology , Institute of Physical Chemistry "Rocasolano", CSIC , 28006 Madrid , Spain
| | - Stefania De Benedetti
- Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , Indiana 46556 , United States
| | - Choon Kim
- Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , Indiana 46556 , United States
| | - Neha Rana
- Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , Indiana 46556 , United States
| | - Mijoon Lee
- Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , Indiana 46556 , United States
| | - Dusan Hesek
- Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , Indiana 46556 , United States
| | - Jed F Fisher
- Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , Indiana 46556 , United States
| | - Julia Sanz-Aparicio
- Department of Crystallography and Structural Biology , Institute of Physical Chemistry "Rocasolano", CSIC , 28006 Madrid , Spain
| | - Juan A Hermoso
- Department of Crystallography and Structural Biology , Institute of Physical Chemistry "Rocasolano", CSIC , 28006 Madrid , Spain
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , Indiana 46556 , United States
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41
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Sanusi ZK, Lawal MM, Govender T, Baijnath S, Naicker T, Maguire GEM, Honarparvar B, Kruger HG. Concerted hydrolysis mechanism of HIV-1 natural substrate against subtypes B and C-SA PR: insight through molecular dynamics and hybrid QM/MM studies. Phys Chem Chem Phys 2020; 22:2530-2539. [PMID: 31942584 DOI: 10.1039/c9cp05639d] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
It is well known that understanding the catalytic mechanism of HIV-1 PR is the rationale on which its inhibitors were developed; therefore, a better understanding of the mechanism of natural substrate hydrolysis is important. Herein, the reaction mechanism of HIV-1 natural substrates with subtypes B and common mutant in South Africa (subtype C-SA) protease were studied through transition state modelling, using a general acid-general base (GA-GB) one-step concerted process. The activation free energies of enzyme-substrate complexes were compared based on their rate of hydrolysis using a two-layered ONIOM (B3LYP/6-31++G(d,p):AMBER) method. We expanded our computational model to obtain a better understanding of the mechanism of hydrolysis as well as how the enzyme recognises or chooses the cleavage site of the scissile bonds. Using this model, a potential substrate-based inhibitor could be developed with better potency. The calculated activation energies of natural substrates in our previous study correlated well with experimental data. A similar trend was observed for the Gag and Gag-Pol natural substrates in the present work for both enzyme complexes except for the PR-RT substrate. Natural bond orbital (NBO) analysis was also applied to determine the extent of charge transfer within the QM part of both enzymes considered and the PR-RT natural substrate. The result of this study shows that the method can be utilized as a dependable computational technique to rationalize lead compounds against specific targets.
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Affiliation(s)
- Zainab K Sanusi
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa.
| | - Monsurat M Lawal
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa.
| | | | - Sooraj Baijnath
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa.
| | - Tricia Naicker
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa.
| | - Glenn E M Maguire
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa. and School of Chemistry and Physics, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Bahareh Honarparvar
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa.
| | - Hendrik G Kruger
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa.
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42
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Whitfield TW, Ragland DA, Zeldovich KB, Schiffer CA. Characterizing Protein-Ligand Binding Using Atomistic Simulation and Machine Learning: Application to Drug Resistance in HIV-1 Protease. J Chem Theory Comput 2020; 16:1284-1299. [PMID: 31877249 DOI: 10.1021/acs.jctc.9b00781] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Over the past several decades, atomistic simulations of biomolecules, whether carried out using molecular dynamics or Monte Carlo techniques, have provided detailed insights into their function. Comparing the results of such simulations for a few closely related systems has guided our understanding of the mechanisms by which changes such as ligand binding or mutation can alter the function. The general problem of detecting and interpreting such mechanisms from simulations of many related systems, however, remains a challenge. This problem is addressed here by applying supervised and unsupervised machine learning techniques to a variety of thermodynamic observables extracted from molecular dynamics simulations of different systems. As an important test case, these methods are applied to understand the evasion by human immunodeficiency virus type-1 (HIV-1) protease of darunavir, a potent inhibitor to which resistance can develop via the simultaneous mutation of multiple amino acids. Complex mutational patterns have been observed among resistant strains, presenting a challenge to developing a mechanistic picture of resistance in the protease. In order to dissect these patterns and gain mechanistic insight into the role of specific mutations, molecular dynamics simulations were carried out on a collection of HIV-1 protease variants, chosen to include highly resistant strains and susceptible controls, in complex with darunavir. Using a machine learning approach that takes advantage of the hierarchical nature in the relationships among the sequence, structure, and function, an integrative analysis of these trajectories reveals key details of the resistance mechanism, including changes in the protein structure, hydrogen bonding, and protein-ligand contacts.
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Affiliation(s)
- Troy W Whitfield
- Department of Medicine , University of Massachusetts Medical School , Worcester , Massachusetts 01605 , United States.,Program in Bioinformatics and Integrative Biology , University of Massachusetts Medical School , Worcester , Massachusetts 01605 , United States
| | - Debra A Ragland
- Department of Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , Worcester , Massachusetts 01605 , United States
| | - Konstantin B Zeldovich
- Program in Bioinformatics and Integrative Biology , University of Massachusetts Medical School , Worcester , Massachusetts 01605 , United States
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , Worcester , Massachusetts 01605 , United States
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43
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Novak J, Grishina MA, Potemkin VA. The Influence of Hydrogen Atoms on the Performance of Radial Distribution Function-Based Descriptors in the Chemoinformatic Studies of HIV-1 Protease Complexes with Inhibitors. Curr Drug Discov Technol 2020; 18:414-422. [PMID: 31899678 DOI: 10.2174/1570163817666200102130415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 11/08/2019] [Accepted: 11/25/2019] [Indexed: 11/22/2022]
Abstract
AIMS The aim of this letter is to explore the influence of adding hydrogen atoms to the crystallographic structures of HIV-1 protease complexes with a series of inhibitors on the performance of radial distribution function based descriptors recently introduced in chemoinformatic studies. BACKGROUND Quite recently the successful application of molecular descriptors based on a radial distribution function to correlate it with biologically interesting properties of a ligand - enzyme complex was demonstrated. Except its predictive power, the analysis of atoms with dominant contributions to the RDFs can be used to identify relevant atoms and interactions. Since original paper was published on dataset consisting of the X-ray structures of complexes without hydrogen atoms, we wonder weather addition of light atoms can provide us new piece of information. OBJECTIVE The primarily objective is to create the model correlating the RDF based descriptors and physicochemical properties of the HIV-1 protease complexes with inhibitors with hydrogen atoms. Then, we will compare the performance of new model with previous one, where the hydrogen atoms were discarded. Information about interactions between the enzyme and the inhibitors will be extracted from the analysis of the RDF. METHODS The radial distribution function descriptor weighted by the number of valence shell electrons has proven to be sensitive to the changes in the structure of the enzyme and enzyme-ligand complexes. For each structure in our data set, RDF will be calculated and using multiple linear regression method the mathematical model will be designed correlating RDF based descriptors and the physicochemical properties. Statistical analysis of the atom's contribution to the total RDF will reveal relevant interactions. RESULTS The applicability of RDF based descriptor for the correlation with pKi and EC50 values is demonstrated, while simple models containing only two or three parameters are able to explain 78 and 86 % of the variance, respectively. The models with explicitly included hydrogens are of comparable quality with the previous models without hydrogens. The analysis of the atom's dominant contributions highlighted the importance of the hydroxyl groups of the inhibitor near the Asp25 and Asp25' residues when it is bounded to the protease. CONCLUSION Models based on the RDF weighted by the number of valence shell electrons for correlating small number of molecular descriptors and physicocehmical properties for structures with and without hydrogens are of comparable quality and both can be used for identification of relevant functional groups and interactions. Other: Our approach can be integrated to the next generation virtual screening methods, because is fast, reliable with high predictability potential.
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Affiliation(s)
- Jurica Novak
- South Ural State University, 20-A, Tchaikovsky Str., Chelyabinsk 454080, Russian Federation
| | - Maria A Grishina
- South Ural State University, 20-A, Tchaikovsky Str., Chelyabinsk 454080, Russian Federation
| | - Vladimir A Potemkin
- South Ural State University, 20-A, Tchaikovsky Str., Chelyabinsk 454080, Russian Federation
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44
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Wang RG, Zhang HX, Zheng QC. Revealing the binding and drug resistance mechanism of amprenavir, indinavir, ritonavir, and nelfinavir complexed with HIV-1 protease due to double mutations G48T/L89M by molecular dynamics simulations and free energy analyses. Phys Chem Chem Phys 2020; 22:4464-4480. [DOI: 10.1039/c9cp06657h] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
MD simulations, MM-PBSA, and SIE analyses were used to investigate the drug resistance mechanisms of two mutations G48T and L89M in HIV-1 protease toward four inhibitors.
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Affiliation(s)
- Rui-Ge Wang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry
- International Joint Research Laboratory of Nano-Micro Architecture Chemistry
- Jilin University
- Changchun 130023
- P. R. China
| | - Hong-Xing Zhang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry
- International Joint Research Laboratory of Nano-Micro Architecture Chemistry
- Jilin University
- Changchun 130023
- P. R. China
| | - Qing-Chuan Zheng
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry
- International Joint Research Laboratory of Nano-Micro Architecture Chemistry
- Jilin University
- Changchun 130023
- P. R. China
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45
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Pedreira JGB, Franco LS, Barreiro EJ. Chemical Intuition in Drug Design and Discovery. Curr Top Med Chem 2019; 19:1679-1693. [PMID: 31258088 DOI: 10.2174/1568026619666190620144142] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/21/2019] [Accepted: 05/23/2019] [Indexed: 12/14/2022]
Abstract
The medicinal chemist plays the most important role in drug design, discovery and development. The primary goal is to discover leads and optimize them to develop clinically useful drug candidates. This process requires the medicinal chemist to deal with large sets of data containing chemical descriptors, pharmacological data, pharmacokinetics parameters, and in silico predictions. The modern medicinal chemist has a large number of tools and technologies to aid him in creating strategies and supporting decision-making. Alongside with these tools, human cognition, experience and creativity are fundamental to drug research and are important for the chemical intuition of medicinal chemists. Therefore, fine-tuning of data processing and in-house experience are essential to reach clinical trials. In this article, we will provide an expert opinion on how chemical intuition contributes to the discovery of drugs, discuss where it is involved in the modern drug discovery process, and demonstrate how multidisciplinary teams can create the optimal environment for drug design, discovery, and development.
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Affiliation(s)
- Júlia G B Pedreira
- Laboratorio de Avaliacao e Sintese de Substancias Bioativas (LASSBio), Instituto de Ciencias Biomedicas (ICB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil.,Programa de Pós-Graduação em Química, UFRJ, Rio de Janeiro, Brazil
| | - Lucas S Franco
- Laboratorio de Avaliacao e Sintese de Substancias Bioativas (LASSBio), Instituto de Ciencias Biomedicas (ICB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil.,Programa de Pós-Graduação em Farmacologia e Química Medicinal, ICB-UFRJ, Rio de Janeiro, Brazil
| | - Eliezer J Barreiro
- Laboratorio de Avaliacao e Sintese de Substancias Bioativas (LASSBio), Instituto de Ciencias Biomedicas (ICB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil.,Programa de Pós-Graduação em Química, UFRJ, Rio de Janeiro, Brazil.,Programa de Pós-Graduação em Farmacologia e Química Medicinal, ICB-UFRJ, Rio de Janeiro, Brazil.,Programa de Pesquisas em Desenvolvimento de Fármacos (PPDF), ICB, UFRJ, Rio de Janeiro, Brazil
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46
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Karnati KR, Wang Y. Structural and binding insights into HIV-1 protease and P2-ligand interactions through molecular dynamics simulations, binding free energy and principal component analysis. J Mol Graph Model 2019; 92:112-122. [PMID: 31351319 DOI: 10.1016/j.jmgm.2019.07.008] [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: 05/22/2019] [Revised: 07/16/2019] [Accepted: 07/17/2019] [Indexed: 12/15/2022]
Abstract
HIV-1 protease (HIV-1-pr) plays an important role in viral replication and maturation, making it one of the most attractive targets for anti-retroviral therapy. To design new effective inhibitors able to combat drug resistance in mutant HIV-1-pr variants, it is essential to gain further understanding about the mechanisms by which the recently proposed inhibitors deactivate the mutant HIV-1-pr variants. In the present work, we explored the interactions between two P2-ligands (DRV, and one new derivative, 4UY) with wild type (WT) and two multiple mutant HIV-1-pr variants (p20 and p51) with all atom molecular dynamics (MD) simulations, binding free energy calculations, and principal component analysis (PCA). The trajectories of MD simulations show that both 4UY and DRV primarily bind with the active sites, flap and 80s loop regions of HIV-1-pr variants through either hydrogen bonds or hydrophobic interactions. More hydrogen bonds and hydrophobic interactions were located for 4UY/HIV-1-pr complexes than for DRV/HIV-1-pr counterparts. More importantly, 4UY was found to have an extra hydrogen bond with the backbone of Gly48' in the flap region of the HIV-1-prs. The flap tip-tip distance (I50-I50') and flap tip-active site distance (I50-D25 and I50'-D25') indicate that the flaps turn more closed in 4UY bound HIV-1-prs than DRV bound ones, and the former also have more compact hydrophobic cavities than the latter. Further, the vector projections from PCA indicate that 4UY/DRV inhibitor binding projects the closing of flap in HIV-1-pr variants. In line with the above trajectory analysis, the thermodynamics calculation with MM-PBSA method suggests much stronger binding affinity for 4UY/HIV-1-pr than DRV/HIV-1-pr by 4.3-6.4 kcal/mol. Although p20 and p51 also induce weaker binding due to multiple mutants for 4UY inhibitor by 1.9-1.8 kcal/mol, their bindings to the new P2 ligand (4UY) are indeed significantly enhanced as compared to DRV. The thermodynamic components responsible for the binding differences and the contribution from key residues to the binding were also discussed in detail.
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Affiliation(s)
- Konda Reddy Karnati
- Department of Chemistry and Forensic Science, Albany State University, Albany, GA, 31705, USA
| | - Yixuan Wang
- Department of Chemistry and Forensic Science, Albany State University, Albany, GA, 31705, USA.
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47
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Sanusi ZK, Lawal MM, Govender T, Maguire GEM, Honarparvar B, Kruger HG. Theoretical Model for HIV-1 PR That Accounts for Substrate Recognition and Preferential Cleavage of Natural Substrates. J Phys Chem B 2019; 123:6389-6400. [DOI: 10.1021/acs.jpcb.9b02207] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Zainab K. Sanusi
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Monsurat M. Lawal
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
| | | | - Glenn E. M. Maguire
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
- School of Chemistry and Physics, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Bahareh Honarparvar
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Hendrik G. Kruger
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
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48
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Ishima R, Kurt Yilmaz N, Schiffer CA. NMR and MD studies combined to elucidate inhibitor and water interactions of HIV-1 protease and their modulations with resistance mutations. JOURNAL OF BIOMOLECULAR NMR 2019; 73:365-374. [PMID: 31243634 PMCID: PMC6941145 DOI: 10.1007/s10858-019-00260-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/19/2019] [Indexed: 06/09/2023]
Abstract
Over the last two decades, both the sensitivity of NMR and the time scale of molecular dynamics (MD) simulation have increased tremendously and have advanced the field of protein dynamics. HIV-1 protease has been extensively studied using these two methods, and has presented a framework for cross-evaluation of structural ensembles and internal dynamics by integrating the two methods. Here, we review studies from our laboratories over the last several years, to understand the mechanistic basis of protease drug-resistance mutations and inhibitor responses, using NMR and crystal structure-based parallel MD simulations. Our studies demonstrate that NMR relaxation experiments, together with crystal structures and MD simulations, significantly contributed to the current understanding of structural/dynamic changes due to HIV-1 protease drug resistance mutations.
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Affiliation(s)
- Rieko Ishima
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Nese Kurt Yilmaz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA.
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49
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Mishin A, Gusach A, Luginina A, Marin E, Borshchevskiy V, Cherezov V. An outlook on using serial femtosecond crystallography in drug discovery. Expert Opin Drug Discov 2019; 14:933-945. [PMID: 31184514 DOI: 10.1080/17460441.2019.1626822] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Introduction: X-ray crystallography has made important contributions to modern drug development but its application to many important drug targets has been extremely challenging. The recent emergence of X-ray free electron lasers (XFELs) and advancements in serial femtosecond crystallography (SFX) have offered new opportunities to overcome limitations of traditional crystallography to accelerate the structure-based drug discovery (SBDD) process. Areas covered: In this review, the authors describe the general principles of X-ray generation and the main properties of XFEL beams, outline details of SFX data collection and processing, and summarize the progress in the development of associated instrumentation for sample delivery and X-ray detection. An overview of the SFX applications to various important drug targets such as membrane proteins is also provided. Expert opinion: While SFX has already made clear advancements toward the understanding of the structure and dynamics of several major drug targets, its robust application in SBDD still needs further developments of new high-throughput techniques for sample production, automation of crystal delivery and data collection, as well as for processing and storage of large amounts of data. The expansion of the available XFEL beamtime is a key to the success of SFX in SBDD.
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Affiliation(s)
- Alexey Mishin
- a Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology , Dolgoprudny , Russia
| | - Anastasiia Gusach
- a Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology , Dolgoprudny , Russia
| | - Aleksandra Luginina
- a Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology , Dolgoprudny , Russia
| | - Egor Marin
- a Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology , Dolgoprudny , Russia
| | - Valentin Borshchevskiy
- a Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology , Dolgoprudny , Russia
| | - Vadim Cherezov
- a Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology , Dolgoprudny , Russia.,b Bridge Institute, Departments of Chemistry and Biological Sciences, University of Southern California , Los Angeles , CA , USA
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50
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Spiriti J, Subramanian SR, Palli R, Wu M, Zuckerman DM. Middle-way flexible docking: Pose prediction using mixed-resolution Monte Carlo in estrogen receptor α. PLoS One 2019; 14:e0215694. [PMID: 31013302 PMCID: PMC6478315 DOI: 10.1371/journal.pone.0215694] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 04/06/2019] [Indexed: 12/17/2022] Open
Abstract
There is a vast gulf between the two primary strategies for simulating protein-ligand interactions. Docking methods significantly limit or eliminate protein flexibility to gain great speed at the price of uncontrolled inaccuracy, whereas fully flexible atomistic molecular dynamics simulations are expensive and often suffer from limited sampling. We have developed a flexible docking approach geared especially for highly flexible or poorly resolved targets based on mixed-resolution Monte Carlo (MRMC), which is intended to offer a balance among speed, protein flexibility, and sampling power. The binding region of the protein is treated with a standard atomistic force field, while the remainder of the protein is modeled at the residue level with a Gō model that permits protein flexibility while saving computational cost. Implicit solvation is used. Here we assess three facets of the MRMC approach with implications for other docking studies: (i) the role of receptor flexibility in cross-docking pose prediction; (ii) the use of non-equilibrium candidate Monte Carlo (NCMC) and (iii) the use of pose-clustering in scoring. We examine 61 co-crystallized ligands of estrogen receptor α, an important cancer target known for its flexibility. We also compare the performance of the MRMC approach with Autodock smina. Adding protein flexibility, not surprisingly, leads to significantly lower total energies and stronger interactions between protein and ligand, but notably we document the important role of backbone flexibility in the improvement. The improved backbone flexibility also leads to improved performance relative to smina. Somewhat unexpectedly, our implementation of NCMC leads to only modestly improved sampling of ligand poses. Overall, the addition of protein flexibility improves the performance of docking, as measured by energy-ranked poses, but we do not find significant improvements based on cluster information or the use of NCMC. We discuss possible improvements for the model including alternative coarse-grained force fields, improvements to the treatment of solvation, and adding additional types of NCMC moves.
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Affiliation(s)
- Justin Spiriti
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR 97239, United States of America
| | - Sundar Raman Subramanian
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, United States of America
| | - Rohith Palli
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, United States of America
| | - Maria Wu
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, United States of America
| | - Daniel M. Zuckerman
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR 97239, United States of America
- * E-mail:
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