RMIT Classification: Trusted
Final Assessment – Drug Discovery in real life
A new pharmaceutical company, Holien-X, is interested in finding new therapeutics for a rare type of children’s cancer, Neuroblastoma. They have gathered over 2000 patients with Neuroblastoma and have also managed to find genetically matched control patients and wish to sequence both to obtain the largest genetic set of data for this disease. Being a rare disease, these patients are very difficult to find, thus the method needs to be as accurate as possible.
Your first step is to decide which technique you will use to sequence this data? To convince Holien-X, you must list why you chose this method and any pros/cons of this method (up to ½ page and/or table/figures).
The sequencing was successful and using differential expression analysis (i.e. comparison between the genes upregulated in Neuroblastoma patients compared to the control patients) Holien-X has discovered the following 3 upregulated targets:
sp|Protein1
MPSCSTSTMPGMICKNPDLEFDSLQPCFYPDEDDFYFGGPDSTPPGEDIWKKFELLPTPP
LSPSRGFAEHSSEPPSWVTEMLLENELWGSPAEEDAFGLGGLGGLTPNPVILQDCMWSGF
SAREKLERAVSEKLQHGRGPPTAGSTAQSPGAGAASPAGRGHGGAAGAGRAGAALPAELA
HPAAECVDPAVVFPFPVNKREPAPVPAAPASAPAAGPAVASGAGIAAPAGAPGVAPPRPG
GRQTSGGDHKALSTSGEDTLSDSDDEDDEEEDEEEEIDVVTVEKRRSSSNTKAVTTFTIT
VRPKNAALGPGRAQSSELILKRCLPIHQQHNYAAPSPYVESEDAPPQKKIKSEASPRPLK
SVIPPKAKSLSPRNSDSEDSERRRNHNILERQRRNDLRSSFLTLRDHVPELVKNEKAAKV
VILKKATEYVHSLQAEEHQLLLEKEKLQARQQQLLKKIEHARTC
sp|Protein2
MASGSCQGCEEDEETLKKLIVRLNNVQEGKQIETLVQILEDLLVFTYSERASKLFQGKNI
HVPLLIVLDSYMRVASVQQVGWSLLCKLIEVCPGTMQSLMGPQDVGNDWEVLGVHQLILK
MLTVHNASVNLSVIGLKTLDLLLTSGKITLLILDEESDIFMLIFDAMHSFPANDEVQKLG
CKALHVLFERVSEEQLTEFVENKDYMILLSALTNFKDEEEIVLHVLHCLHSLAIPCNNVE
VLMSGNVRCYNIVVEAMKAFPMSERIQEVSCCLLHRLTLGNFFNILVLNEVHEFVVKAVQ
QYPENAALQISALSCLALLTETIFLNQDLEEKNENQENDDEGEEDKLFWLEACYKALTWH
RKNKHVQEAACWALNNLLMYQNSLHEKIGDEDGHFPAHREVMLSMLMHSSSKEVFQASAN
ALSTLLEQNVNFRKILLSKGIHLNVLELMQKHIHSPEVAESGCKMLNHLFEGSNTSLDIM
AAVVPKILTVMKRHETSLPVQLEALRAILHFIVPGMPEESREDTEFHHKLNMVKKQCFKN
DIHKLVLAALNRFIGNPGIQKCGLKVISSIVHFPDALEMLSLEGAMDSVLHTLQMYPDDQ
EIQCLGLSLIGYLITKKNVFIGTGHLLAKILVSSLYRFKDVAEIQTKGFQTILAILKLSA
SFSKLLVHHSFDLVIFHQMSSNIMEQKDQQFLNLCCKCFAKVAMDDYLKNVMLERACDQN
NSIMVECLLLLGADANQAKEGSSLICQVCEKESSPKLVELLLNSGSREQDVRKALTISIG
KGDSQIISLLLRRLALDVANNSICLGGFCIGKVEPSWLGPLFPDKTSNLRKQTNIASTLA
RMVIRYQMKSAVEEGTASGSDGNFSEDVLSKFDEWTFIPDSSMDSVFAQSDDLDSEGSEG
SFLVKKKSNSISVGEFYRDAVLQRCSPNLQRHSNSLGPIFDHEDLLKRKRKILSSDDSLR
SSKLQSHMRHSDSISSLASEREYITSLDLSANELRDIDALSQKCCISVHLEHLEKLELHQ
NALTSFPQQLCETLKSLTHLDLHSNKFTSFPSYLLKMSCIANLDVSRNDIGPSVVLDPTV
KCPTLKQFNLSYNQLSFVPENLTDVVEKLEQLILEGNKISGICSPLRLKELKILNLSKNH
ISSLSENFLEACPKVESFSARMNFLAAMPFLPPSMTILKLSQNKFSCIPEAILNLPHLRS
LDMSSNDIQYLPGPAHWKSLNLRELLFSHNQISILDLSEKAYLWSRVEKLHLSHNKLKEI
PPEIGCLENLTSLDVSYNLELRSFPNEMGKLSKIWDLPLDELHLNFDFKHIGCKAKDIIR
FLQQRLKKAVPYNRMKLMIVGNTGSGKTTLLQQLMKTKKSDLGMQSATVGIDVKDWPIQI
RDKRKRDLVLNVWDFAGREEFYSTHPHFMTQRALYLAVYDLSKGQAEVDAMKPWLFNIKA
RASSSPVILVGTHLDVSDEKQRKACMSKITKELLNKRGFPAIRDYHFVNATEESDALAKL
RKTIINESLNFKIRDQLVVGQLIPDCYVELEKIILSERKNVPIEFPVIDRKRLLQLVREN
QLQLDENELPHAVHFLNESGVLLHFQDPALQLSDLYFVEPKWLCKIMAQILTVKVEGCPK
HPKGIISRRDVEKFLSKKRKFPKNYMSQYFKLLEKFQIALPIGEEYLLVPSSLSDHRPVI
ELPHCENSEIIIRLYEMPYFPMGFWSRLINRLLEISPYMLSGRERALRPNRMYWRQGIYL
NWSPEAYCLVGSEVLDNHPESFLKITVPSCRKGCILLGQVVDHIDSLMEEWFPGLLEIDI
CGEGETLLKKWALYSFNDGEEHQKILLDDLMKKAEEGDLLVNPDQPRLTIPISQIAPDLI
LADLPRNIMLNNDELEFEQAPEFLLGDGSFGSVYRAAYEGEEVAVKIFNKHTSLRLLRQE
LVVLCHLHHPSLISLLAAGIRPRMLVMELASKGSLDRLLQQDKASLTRTLQHRIALHVAD
GLRYLHSAMIIYRDLKPHNVLLFTLYPNAAIIAKIADYGIAQYCCRMGIKTSEGTPGFRA
PEVARGNVIYNQQADVYSFGLLLYDILTTGGRIVEGLKFPNEFDELEIQGKLPDPVKEYG
CAPWPMVEKLIKQCLKENPQERPTSAQVFDILNSAELVCLTRRILLPKNVIVECMVATHH
NSRNASIWLGCGHTDRGQLSFLDLNTEGYTSEEVADSRILCLALVHLPVEKESWIVSGTQ
SGTLLVINTEDGKKRHTLEKMTDSVTCLYCNSFSKQSKQKNFLLVGTADGKLAIFEDKTV
KLKGAAPLKILNIGNVSTPLMCLSESTNSTERNVMWGGCGTKIFSFSNDFTIQKLIETRT
SQLFSYAAFSDSNIITVVVDTALYIAKQNSPVVEVWDKKTEKLCGLIDCVHFLREVMVKE
NKESKHKMSYSGRVKTLCLQKNTALWIGTGGGHILLLDLSTRRLIRVIYNFCNSVRVMMT
AQLGSLKNVMLVLGYNRKNTEGTQKQKEIQSCLTVWDINLPHEVQNLEKHIEVRKELAEK
MRRTSVE
sp|Protein3
MNNFGNEEFDCHFLDEGFTAKDILDQKINEVSSSDDKDAFYVADLGDILKKHLRWLKALP
RVTPFYAVKCNDSKAIVKTLAATGTGFDCASKTEIQLVQSLGVPPERIIYANPCKQVSQI
KYAANNGVQMMTFDSEVELMKVARAHPKAKLVLRIATDDSKAVCRLSVKFGATLRTSRLL
LERAKELNIDVVGVSFHVGSGCTDPETFVQAISDARCVFDMGAEVGFSMYLLDIGGGFPG
SEDVKLKFEEITGVINPALDKYFPSDSGVRIIAEPGRYYVASAFTLAVNIIAKKIVLKEQ
TGSDDEDESSEQTFMYYVNDGVYGSFNCILYDHAHVKPLLQKRPKPDEKYYSSSIWGPTC
DGLDRIVERCDLPEMHVGDWMLFENMGAYTVAAASTFNGFQRPTIYYVMSGPAWQLMQQF
QNPDFPPEVEEQDASTLPVSCAWESGMKRHRAACASASINV
Identify and compare these 3 potential targets and decide which one you would choose for a drug discovery campaign. To convince Holien-X, you must list the pros/cons of this target and show evidence for why this target is the best for a drug discovery campaign (approx. ½ - 1 page + figures/ tables).
Holien-X has re-analysed their data using network-based methods and discovered new information which shows that Aurora Kinase B (Uniprot code: Q96GD4) is the best druggable option as it is:
· highly expressed and upregulated in the diseased patients compared to controls
· has close homology to mouse
· has a close homolog to construct a high quality homology model
· has a known role in cance
Your job is to download the alphafold homology model and confirm its suitability for a drug discovery campaign. For example, you may like to; analyse the quality of this model (i.e. https:
swissmodel.expasy.org/assess), analyse the properties of the protein, search for druggable pockets etc. Write these details into your report with figures to guide the team at Holien-X (approx. ½ - 1 page + figures/tables).
Holien-X has taken your advice on board and would like to conduct a Virtual Screen. Write a short proposal for the steps you will undertake in order to do this (up to ½ page and/or table/figures)
Congratulation, your virtual screen was successful. Holien-X has screened the compounds you suggested and has identified 5 compounds which bind to the wild-type protein but not an A105R mutant isoform (confirming your active site). They also reduce the growth of Neuroblastoma cell culture.
Analyse the following table and let Holien-X know which compound you would choose to develop further and why? (up to ½ page and/or table/figures)
SMILES String
Activity (IC50)
O=C(C1=CC=CC(Cl)=C1F)N(CC2)CCN2CC3=CC=CC(CC4=NC=CS4)=N3
1nM
CN(C)CC1=CC(C2=CC(C(C3=CN(CC)N=C3C4=CC=CC=C4)=NC=N5)=C5N2)=CC=C1
0.5nM
CCN1N=C(C2=CC=C(F)C=C2)C([C@H]3CCCC(C(F)(F)F)C3)=C1
1.5nM
O=C(NC1=CCC=C([C@H]2CCOC2)C1)C3=NC=CN=C3
1mM
O=[N+]([O-])C1=CC=C(C2=NNC(SCC#CC)=N2)C=C1C
1mM
Holien-X has now developed your compound into Phase 2 clinical trials. Unfortunately, they are finding a subset of patients which are showing resistance to the drug. They have sequenced these patients, and all have the following nucleotide sequence.
MutantProtein
atggcgcagaaagaaaacagctatccgtggccgtatggccgccagaccgcgccgagcggc
ctgagcaccctgccgcagcgcgtgctgcgcaaagaaccggtgaccccgagcgcgctggtg
ctgatgagccgcagcaacgtgcagccgaccgcggcgccgggccagaaagtgatggaaaac
agcagcggcaccccggatattctgacccgccattttaccattgatgattttgaaattggc
cgcccgctgggcaaaggcaaatttggcaacgtgtatctggcgcgcgaaaaaaaaagccat
tttattgtggcgctgaaagtgctgtttaaaagccagattgaaaaagaaggcgtggaacat
cagctgcgccgcgaaattgaaattcaggcgcatctgcatcatccgaacattgaacgcctg
tataactatttttatgatcgccgccgcatttatctgattctggaatatgcgccgcgcggc
gaactgtataaagaactgcagaaaagctgcacctttgatgaacagcgcaccgcgaccatt
atggaagaactggcggatgcgctgatgtattgccatggcaaaaaagtgattcatcgcgat
attaaaccggaaaacctgctgctgggcctgaaaggcgaactgaaaattgcggattttggc
tggagcgtgcatgcgccgagcctgcgccgcaaaaccatgtgcggcaccctggattatctg
ccgccggaaatgattgaaggccgcatgcataacgaaaaagtggatctgtggtgcattggc
gtgctgtgctatgaactgctggtgggcaacccgccgtttgaaagcgcgagccataacgaa
acctatcgccgcattgtgaaagtggatctgaaatttccggcgagcgtgccgatgggcgcg
caggatctgattagcaaactgctgcgccataacccgagcgaacgcctgccgctggcgcag
gtgagcgcgcatccgtgggtgcgcgcgaacagccgccgcgtgctgccgccgagcgcgctg
cagagcgtggcg
Holien-X would like to understand what the patient mutant is? Is it a modest mutation or significant? Where on the protein this mutation is occu
ing? Is it likely to influence compound binding or another aspect of the protein function? (½-1 page + table/figures
Congratulations based on your analysis the drug has now passed all approvals and is being used to treat these patients. Please add a summary sentence or two describing how you feel bioinformatics helped these patients.