Qifeng Bai

Qifeng Bai
Lanzhou University | LZU · School of Basic Medical Sciences

Professor

About

66
Publications
8,121
Reads
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700
Citations
Citations since 2016
32 Research Items
650 Citations
2016201720182019202020212022050100150
2016201720182019202020212022050100150
2016201720182019202020212022050100150
2016201720182019202020212022050100150

Publications

Publications (66)
Article
Smoothened (SMO) is an attractive therapeutic target for the treatment and prevention of several malignant tumors of the nervous system. The crystal structure of SMO shows cholesterol interacts with residue Asp95 via the noncovalent bond. However, some studies indicate that cholesterol covalently binds to residue Asp95 of SMO. To study these contra...
Article
Full-text available
Improving drug discovery efficiency is a core and long-standing challenge in drug discovery. For this purpose, many graph learning methods have been developed to search potential drug candidates with fast speed and low cost. In fact, the pursuit of high prediction performance on a limited number of datasets has crystallized their architectures and...
Article
Repositioning or repurposing drugs account for a substantial part of entering approval pipeline drugs, which indicates that drug repositioning has huge market potential and value. Computational technologies such as machine learning methods have accelerated the process of drug repositioning in the last few decades years. The repositioning potential...
Preprint
Full-text available
Improving drug discovery efficiency is a core and long-standing challenge in drug discovery. For this purpose, many graph learning methods have been developed to search potential drug candidates with fast speed and low cost. In fact, the pursuit of high prediction performance on a limited number of datasets has crystallized them, making them lose a...
Article
Full-text available
De novo drug design is a stationary way to build novel ligands in the confined pocket of receptor by assembling the atoms or fragments, while molecular dynamics (MD) simulation is a dynamical way to study the interaction mechanism between the ligands and receptors based on the molecular force field. De novo drug design and MD simulation are effecti...
Article
Full-text available
Activation of human free fatty acid receptor 1 (FFAR1, also called hGPR40) enhances insulin secretion in a glucose-dependent manner. Hence, the development of selective agonist targeting hGPR40 has been proposed as a therapeutic strategy of type 2 diabetes mellitus. Some agonists targeting hGPR40 were reported. The radioligand-binding studies and t...
Article
Full-text available
Artificial intelligence can train the related known drug data into deep learning models for drug design, while classical algorithms can design drugs through established and predefined procedures. Both deep learning and classical algorithms have their merits for drug design. Here, the webserver WADDAICA is built to employ the advantage of deep learn...
Article
Full-text available
Deep learning is an important branch of artificial intelligence that has been successfully applied into medicine and two-dimensional ligand design. The three-dimensional (3D) ligand generation in the 3D pocket of protein target is an interesting and challenging issue for drug design by deep learning. Here, the MolAICal software is introduced to sup...
Preprint
Full-text available
Deep learning methods have permeated into the research area of computer-aided drug design. The deep learning generative model and classical algorithm can be simultaneously used for three-dimensional (3D) drug design in the 3D pocket of the receptor. Here, three aspects of MolAICal are illustrated for drug design: in the first part, the MolAICal use...
Article
Full-text available
Foot-and-mouth disease virus (FMDV), the most acid-unstable virus among picornaviruses, tends to disassemble into pentamers at pH values slightly below neutrality. However, the structural integrity of intact virion is one of the most important factors that influence the induction of a protective antibody response. Thus, improving the acid stability...
Article
CC chemokine receptor 2 (CCR2) and its endogenous CC chemokine ligands are associated with numerous inflammatory, neurodegenerative diseases, and cancer. CCR2 is becoming an attractive target in the treatment of autoimmune disease and neurodegenerative diseases. The orthosteric antagonist BMS-681 and allosteric antagonist CCR2-RA-[R] of CCR2 show p...
Article
Full-text available
The inactive conformations of glucagon receptor (GCGR) are widely reported by crystal structures that support the precision structure for drug discovery of type 2 diabetes. The previous study shows that the intracellular part is open in the glucagon-bound GCGR (glu-GCGR) and closed in the apo-GCGR by accelerated molecular dynamics (aMD) simulations...
Article
Full-text available
Recently, small-molecule compounds have been reported to block the PD-1/PD-L1 interaction by inducing the dimerization of PD-L1. All these inhibitors had a common scaffold and interacted with the cavity formed by two PD-L1 monomers. This special interactive mode provided clues for the structure-based drug design, however, also showed limitations fo...
Article
Full-text available
The smoothened receptor (Smo) plays a key role in Hedgehog (Hh) signaling pathway and it has been regarded as an efficacious therapeutic target for basal cell carcinoma (BCC) and medulloblastoma (MB). Nevertheless, the resistance mutation and active mutants of Smo have put forward the requirement of finding more effective inhibitors. Herein, we per...
Article
As one member of class B G protein-coupled receptors (GPCRs), the glucagon-like peptide-1 (GLP-1) can regulate the blood glucose level by binding to the glucagon-like peptide-1 receptor (GLP-1R). Since the extracellular domain (ECD) of GLP-1R is considered as one of binding sites of GLP-1, the open and closed states of ECD play an important role in...
Article
Full-text available
The sequence variation within the capsid proteins occurs frequently in the infection of susceptible tissue cultures, reflecting the high levels of genetic diversity of FMDV. A systematic study for the functional significance of isolate-specific residues in VP0 and VP3 of FMDV PanAsia-1 strains suggested that the interaction of amino acid side chain...
Article
The opioid receptors belong to the class A seven transmembrane-spanning (7TM) G protein-coupled receptors (GPCRs). The κ-opioid receptor (KOR) is a subfamily of four opioid receptors. The endogenous peptide and a variety of selective agonists and antagonists of KOR have been developed. The structurally similar ligands at the same site cause complet...
Article
Big data research has become popular and exciting studies in almost all scientific fields such as biology, chemistry, epidemiology, medicine and drug discovery. The various systems and platforms produce large amounts of data every day. It will be very helpful for the researchers and workers to deal with big data if the practical database and useful...
Article
Full-text available
The FDA approved drug suvorexant binds to the horseshoe shape pocket of OX2R with the boat conformation. The horseshoe shape pocket plays an important role on the biological activity of OX2R in the cell membrane. To study the binding mechanism between the horseshoe shape pocket of OX2R and boat conformation of suvorexant, the crystal structures of...
Article
Full-text available
ᅟ This review summarized the molecular determinants of the acid stability of FMDV in order to explore the uncoating mechanism of FMDV and improve the acid stability of vaccines. Background The foot-and-mouth disease virus (FMDV) capsid is highly acid labile and tends to dissociate into pentameric subunits at acidic condition to release viral RNA f...
Article
As co-chaperones of the 90-kDa heat shock protein(HSP90), FK506 binding protein 51 (FKBP51) and FK506 binding protein 52 (FKBP52) modulate the maturation of steroid hormone receptor through their specific FK1 domains (FKBP12-like domain 1). The inhibitors targeting FK1 domains are potential therapies for endocrine-related physiological disorders. H...
Article
Resveratrol and its derivatives have been shown to display beneficial effects to neurodegenerative diseases. However, the molecular mechanism of resveratrol and its derivatives on prion conformational conversion is poorly understood. In this work, the interaction mechanism between prion and resveratrol as well as its derivatives were investigated u...
Article
The accumulation of intrinsically disordered α-synuclein (αS) protein that can form β-sheet-rich fibrils is linked to Parkinson diseases (PD). (-)-Epigallocatechin-3-gallate (EGCG) is the most abundant active component in green tea and can inhibit the fibrillation of αS. The elucidation of this molecular mechanism will be helpful to understand the...
Article
Full-text available
Higher-order structures of the actin cytoskeleton are essential for pollen germination and pollen tube growth. ACTIN-DEPOLYMERIZING FACTORs (ADFs) typically contribute to actin turnover by severing/depolymerizing actin filaments. Recently, we demonstrated that Arabidopsis subclass III ADFs (ADF5 and ADF9) evolved F-actin bundling function from cons...
Article
Full-text available
Most proinflammatory actions of C-reactive protein (CRP) are only expressed following dissociation of its native pentameric assembly into monomeric form (mCRP). However, little is known about what underlies the greatly enhanced activities of mCRP. Here we show that a single sequence motif, i.e. cholesterol binding sequence (CBS; a.a. 35-47), is res...
Article
Full-text available
Metabotropic glutamate receptor 1 (mGlu1), which belongs to class C G protein-coupled receptors (GPCRs), can be coupled with G protein to transfer extracellular signal by dimerization and allosteric regulation. Unraveling the dimer packing and allosteric mechanism can be of great help for understanding specific regulatory mechanism and designing mo...
Article
Full-text available
As a promising target for the treatment of lung cancer, the MutT Homolog 1 (MTH1) protein can be inhibited by crizotinib. A recent work shows that the inhibitory potency of (S)-crizotinib against MTH1 is about 20 times over that of (R)-crizotinib. But the detailed molecular mechanism remains unclear. In this study, molecular dynamics (MD) simulatio...
Data
Convergence of the potentials of mean force (PMFs), and it is convergent. (TIF)
Data
Atom types and partial charges for (R)-crizotinib. (DOC)
Data
Superposition of the stable structure extracted from equilibrium trajectory with the X-ray structure. A. (S)-crizotinib/MTH1 protein complex; B. (R)-crizotinib/MTH1 protein complex. (TIF)
Data
Atom types and partial charges for (S)-crizotinib. (DOC)
Article
Full-text available
The villin/gelsolin/fragmin superfamily is a major group of Ca2+-dependent actin-binding proteins (ABPs) involved in various cellular processes. Members of this superfamily typically possess three or six tandem gelsolin-like (G) domains, and each domain plays a distinct role in actin filament dynamics. Although the activities of most G domains have...
Article
JAK2 plays pivotal role in the tumorigenesis of STAT3 constitutively activated solid tumors. JAK2 mutations are involved in the pathogenesis of various types of hematopoietic disorders such as myeloproliferative disorders (MPDs), polycythemia vera (PV), essential thoursombocythemia (ET) and primary myelofibrosis (PMF). Thus, small molecular inhibit...
Article
C-C chemokine receptor type 5 (CCR5) is the co-receptor of human immunodeficiency virus type 1 (HIV-1) and plays an important role in HIV-1 virus infection. Maraviroc has been proved to be effective for anti-HIV-1 by targeting CCR5. Understanding the detailed interaction mechanism between CCR5 and Maraviroc will be of great help to the rational des...
Article
Full-text available
We designed a program called MolGridCal that can be used to screen small molecule database in grid computing on basis of JPPF grid environment. Based on MolGridCal program, we proposed an integrated strategy for virtual screening and binding mode investigation by combining molecular docking, molecular dynamics (MD) simulations and free energy calcu...
Article
Background : The SMO receptor, one of Class F GPCRs, is an essential component of the canonical hedgehog signaling pathway which plays a key role in the regulation of embryonic development in animals. The function of the SMO receptor can be modulated by small-molecule agonists and antagonists, some of which are potential antitumour agents. Understa...
Article
Full-text available
The reported crystal structures of β2 adrenergic receptor (β2AR) reveal that the open and closed states of the water channel are correlated with the inactive and active conformations of β2AR. However, more details about the process by which the water channel states are affected by the active to inactive conformational change of β2AR remain illusive...
Article
Full-text available
Corticotropin-releasing factor receptor 1 (CRF1R), a member of class B G-protein-coupled receptors (GPCRs), plays an important role in the treatment of osteoporosis, diabetes, depression, migraine and anxiety. To explore the escape pathway of the antagonist CP-376395 in the binding pocket of CRF1R, molecular dynamics (MD) simulations, dynamical net...
Article
Full-text available
Prion diseases are marked by cerebral accumulation of the abnormal isoform of the prion protein. A fragment of prion protein composed of residues 106-126 (PrP106-126) exhibits similar properties to full length prion and plays a key role in the conformational conversion from cellular prion to its pathogenic pattern. Soluble oligomers of PrP106-126 h...
Article
Full-text available
Epidermal growth factor receptor (EGFR) is a clinical therapeutic target to treat a subset of NSCLC harboring EGFR mutants. However, some patients with similar kind of EGFR mutation show intrinsic resistance to TKIs. It indicates that other key molecules are involved in the survival of these cancer cells. We showed here that TPCA-1, a previously re...
Article
GPU computing is the use of a graphics processing unit together with a CPU to accelerate large scale scientific and engineering applications, such as molecule simulation. The paper use NVIDIA Tesla C2050, NVIDIA GTX580 and NAMD 2.9 simulates three differences molecule systems: Beta2,SET9 and Ubiquitin. We compared and analyzed the results of the si...
Article
Full-text available
β2 adrenergic receptor (β2AR) regulated many key physiological processes by activation of a heterotrimeric GTP binding protein (Gs protein). This process could be modulated by different types of ligands. But the details about this modulation process were still not depicted. Here, we performed molecular dynamics (MD) simulations on the structures of...
Data
Time evolution of RMSD of the backbone atoms of α5-helix and TM 3,5,6,7. (TIF)
Data
Interactive Essential Dynamics. (DOC)
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Speed test of GPU workstation. Workstation with 12 Cores+4GPU gives the fastest speed. (TIF)
Data
RMSD of simulated conformational backbone atoms with respect to the crystal structure of ICI 118,551-bound β2AR. (DOC)
Data
Membrane building protocol. (DOC)
Data
RMSD of backbone atoms of β2AR versus 5 ns MD simulations time. (TIF)
Data
Animation about the separation or association of Gαs and Gβγ induced by different ligands. (AVI)
Data
The crystal structures of SET9 in complex with H3 and p53. (A) The complex of SET9 and H3 peptides. The water colored red forms hydrogen bonds with Y305, G292 and A295. This figure was made by 1O9S file which was extracted from Protein Data Bank (PDB). (B) The complex of SET9 and p53 peptides. The water colored blue forms the same hydrogen bonds wi...
Data
The structures of AdoHcy and AdoMet. (TIF)
Data
The distances between atoms of p53-K372 (DOC)