Task instructionsDownload theinstructionsDownload instructionsand complete the questions. Each question has a guide for how long it should be. Please use this as a guide, however you will be assessed...

Task instructions

Download the
instructions


Download instructions

and complete the questions. Each question has a guide for how long it should be. Please use this as a guide, however you will be assessed on your ability to give succinct, but informative reports.

Learning Outcomes

The Learning Outcomes for this assessment are:

• Explain the basic principles that underpin Bioinformatics analyses, and apply these principles when analysing biological data;


• Analyse biological data using a variety of Bioinformatics tools; and


• Interpret correctly the outputs from tools used to analyse biological data and make meaningful predictions from these outputs.

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 cancer 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 occurring? 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.